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首页自然科学物理学分子模拟:从算法到应用(第2版)(英文版)物理学经典 ELSEVIER 爱思唯尔 Understanding Molecular Simulation: From Algorithms to Applications Second Edition

分子模拟:从算法到应用(第2版)(英文版)物理学经典 ELSEVIER 爱思唯尔 Understanding Molecular Simulation: From Algorithms to Applications Second Edition

从算法到应用,从代码到突破;解码分子世界的计算密码,赋能科学与工业创新!

作者:〔荷〕达恩 · 弗伦克尔(Daan Frenkel)〔荷〕贝伦德 · 斯密特(Berend Smit) 出版社:世界图书出版公司 出版时间:2025年04月  原版书名:Understanding Molecular Simulation: From Algorithms to Applications 

ISBN: 9787523218570
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EUR €73.99

类别: 自然科学 新书热卖榜, 物理学 SKU:6861800632b4b56dec0af603 库存: 有现货
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描述

开 本: 16开纸 张: 胶版纸包 装: 平装-胶订是否套装: 否国际标准书号ISBN: 9787523218570

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内容简介

由达恩·弗伦克尔和贝伦德·斯密特所著的《分子模拟:从算法到应用》解释了材料科学分子模拟背后的物理学。由于计算机模拟人员一直面临着为特定应用选择特定技术的问题,并且现有的工具种类繁多,所以在选择技术时需要充分了解基本原理。更重要的是,这种对基本原理的理解可以大大提高仿真程序的效率。除了带领读者了解这些程序背后的原理之外,本书还介绍了一些经常被应用的技巧和经验,这些技巧和经验在仿真中是“常识”般的存在。掌握它们并了解其背后原理,就可以根据实际问题迅速选择合适的技巧。本书的读者对象是活跃在计算机仿真领域或计划成为计算机仿真领域的人士。

作者简介

达恩·弗伦克尔(Daan Frenkel)是剑桥大学化学名誉教授,曾任剑桥大学化学系主任和研究主任。分别在1972年和1977年于荷兰阿姆斯特丹大学获得物理化学的硕士和博士学位。1999年获得英国皇家化学学会伯克讲师和奖章。2007年荣获欧洲物理学会 Alder-CECAM 计算机模拟奖。2008年当选美国人文与科学院外籍荣誉院士。2016年当选美国国家科学院外籍院士,同年获得玻尔兹曼奖章(IUPAP)。

 

贝伦德·斯密特(Berend Smit)是瑞士洛桑联邦理工学院(EPFL)化学工程与化学教授、化学与生物分子工程兼职教授、美国加州大学伯克利分校化学兼职教授。他于1987年获得荷兰代尔夫特理工大学化学工程硕士学位和物理学硕士学位。1990年获得荷兰乌得勒支大学化学博士学位。1997—2007 年在荷兰阿姆斯特丹大学担任计算化学教授。2004年,他当选为法国里昂欧洲原子与分子计算中心(CECAM)主任。自 2007 年起,他担任加州大学伯克利分校化学工程和化学教授,以及劳伦斯伯克利国家实验室材料科学部的化学教员。自 2014 年以来,他一直担任 EPFL 能源中心主任。

目  录

Preface to the Second Edition

Preface

List of Symbols

1 Introduction

Part I Basics

2 Statistical Mechanics

2.1 Entropy and Temperature

2.2 Classical Statistical Mechanics

2.2.1 Ergodicity

2.3 Questions and Exercises

3 Monte Carlo Simulations

3.1 The Monte Carlo Method

3.1.1 Importance Sampling

3.1.2 The Metropolis Method

3.2 A Basic Monte Carlo Algorithm

3.2.1 The Algorithm

3.2.2 Technical Details

3.2.3 Detailed Balance versus Balance

3.3 Trial Moves

3.3.1 Translational Moves

3.3.2 Orientational Moves

3.4 Applications

3.5 Questions and Exercises

4 Molecular Dynamics Simulations

4.1 Molecular Dynamics: The Idea

4.2 Molecular Dynamics: A Program

4.2.1 Initialization

4.2.2 The Force Calculation

4.2.3 Integrating the Equations of Motion

4.3 Equations of Motion

4.3.1 Other Algorithms

4.3.2 Higher-Order Schemes

4.3.3 Liouville Formulation of Time-Reversible Algorithm

4.3.4 Lyapunov Instability

4.3.5 One More Way to Look at the Verlet Algorithm

4.4 Computer Experiments

4.4.1 Diffusio

4.4.2 Order-n Algorithm to Measure Correlations

4.5 Some Applications

4.6 Questions and Exercises

Part II Ensembles

5 Monte Carlo Simulations in Various Ensembles

5.1 General Approach

5.2 Canonical Ensemble

5.2.1 Monte Carlo Simulations

5.2.2 Justification of the Algorithm

5.3 Microcanonical Monte Carlo

5.4 Isobaric-lsothermal Ensemble

5.4.1 Statistical Mechanical Basis

5.4.2 Monte Carlo Simulations

5.4.3 Applications

5.5 Isotension-Isothermal Ensemble

5.6 Grand-Canonical Ensemble

5.6.1 Statistical Mechanical Basis

5.6.2 Monte Carlo Simulations

5.6.3 Justification of the Algorithm

              5.6.4 Applications

5.7 Questions and Exercises

6 Molecular Dynamics in Various Ensembles

6.1 Molecular Dynamics at Constant Temperature

6.1.1 The Andersen Thermostat

6.1.2 Nosé-Hoover Thermostat

6.1.3 Nosé-Hoover Chains

6.2 Molecular Dynamics at Constant Pressure

6.3 Questions and Exercises

Part III Free Energies and Phase Equilibria

7 Free Energy Calculations

7.1 Thermodynamic Integration

7.2 Chemical Potentials

7.2.1 The Particle Isertion Method

7.2.2 Other Ensembles

7.2.3 Overlapping Distribution Method

7.3 Other Free Energy Methods

7.3.1 Multiple Histograms

7.3.2 Acceptance Ratio Method

7.4 Umbrella Samplin

7.4.1 Nonequilibrium Free Energy Methods

7.5 Questions and Exercises

8 The Gibbs Ensemble

8.1 The Gibbs Ensemble Technique

8.2 The Partition Function

8.3 Monte Carlo Simulations

8.3.1 Particle Displacement

8.3.2 Volume Change

8.3.3 Particle Exchange

8.3.4 Implementation

8.3.5 Analyzing the Results

8.4 Applications

8.5 Questions and Exercises

9 Other Methods to Study Coexistence

9.1 Semigrand Ensemble

9.2 Tracing Coexistence Curves

10 Free Energies of Solids

10.1 Thermodynamic Itegration

10.2 Free Energies of Solids

10.2.1 Atomic Solids with Continuous Potentials

10.3 Free Energies of Molecular Solids

10.3.1 Atomic Solids with Discontinuous Potentials

10.3.2 General Implementation Issues

10.4 Vacancies and Interstitials

10.4.1 Free Energies

10.4.2 Numerical Calculations

11 Free Energy of Chain Molecules

11.1 Chemical Potential as Reversible Work

11.2 Rosenbluth Sampling

11.2.1 Macromolecules with Discrete Conformations

11.2.2 Extension to Continuously Deformable Molecules

11.2.3 Overlapping Distribution Rosenbluth Method

11.2.4 Recursive Sampling

11.2.5 Pruned-Enriched Rosenbluth Method

Part IV Advanced Techniques

12 Long-Range Interactions

12.1 Ewald Sums

12.1.1 Point Charges

12.1.2 Dipolar Particles

12.1.3 Dielectric Constant

12.1.4 Boundary Conditions

12.1.5 Accuracy and Computational Complexity

12.2 Fast Multipole Method

12.3 Particle Mesh Approaches

12.4 Ewald Summation in a Slab Geometry

13 Biased Monte Carlo Schemes

13.1 Biased Sampling Techniques

13.1.1 Beyond Metropolis

13.1.2 Orientational Bias

13.2 Chain Molecules

13.2.1 Configurational-Bias Monte Carlo

13.2.2 Lattice Models

13.2.3 Off-lattice Case

13.3 Generation of Trial Orientations

13.3.1 Strong Intramolecular Interactions

13.3.2 Generation of Branched Molecules

13.4 Fixed Endpoints

13.4.1 Lattice Models

13.4.2 Fully Flexible Chain

13.4.3 Strong Intramolecular Interactions

13.4.4 Rebridging Monte Carlo

13.5 Beyond Polymers

13.6 Other Ensembles

13.6.1 Grand-Canonical Ensemble

13.6.2 Gibbs Ensemble Simulations

13.7 Recoil Growth

13.7.1 Algorithm

13.7.2 Justification of the Method

13.8 Questions and Exercises

14 Accelerating Monte Carlo Sampling

14.1 Parallel Tempering

14.2 Hybrid Monte Carlo

14.3 Cluster Moves

14.3.1 Clusters

14.3.2 Early Rejection Scheme

15 Tackling Time-Scale Problems

15.1 Constraints

15.1.1 Constrained and Unconstrained Averages

15.2 On-the-Fly Optimization: Car-Parrinello Approach

15.3 Multiple Time Steps

16 Rare Events

16.1 Theoretical Background

16.2 Bennett-Chandler Approach

16.2.1 Computational Aspects

16.3 Diffusive Barrier Crossing

16.4 Transition Path Ensemble

16.4.1 Path Ensemble

16.4.2 Monte Carlo Simulations

16.5 Searching for the Saddle Point

17 Dissipative Particle Dynamics

17.1 Description of the Technique

17.1.1 Justification of the Method

17.1.2 Implementation of the Method

17.1.3 DPD and Energy Conservation

17.2 Other Coarse-Grained Techniques

Part V Appendices

A Lagrangian and Hamiltonian

A.1 Lagrangian

A.2 Hamiltonian

A.3 Hamilton Dynamics and Statistical Mechanics

A.3.1 Canonical Transformation

A.3.2 Symplectic Condition

A.3.3 Statistical Mechanics

B Non-Hamiltonian Dynamics

B.1Theoretical Background

B.2 Non-Hamiltonian Simulation of the N, V, T Ensemble

B.2.1 The Nosé-Hoover Algorithm

B.2.2 Nosé-Hoover Chains

B.3 The N, P, T Ensemble

C Linear Response Theory

C.1 Static Response

C.2 Dynamic Response

C.3 Dissipation

C.3.1 Electrical Conductivity

C.3.2 Viscosity

C.4 Elastic Constants

D Statistical Errors

D.1 Static Properties: System Size

D.2 Correlation Functions

D.3 Block Averages

E Integration Schemes

E.1 Higher-Order Schemes

E.2 Nosé-Hoover Algorithms

E.2.1 Canonical Ensemble

E.2.2 The Isothermal-Isobaric Ensemble

F Saving CPU Time

F.1 Verlet List

F.2 Cell Lists

F.3 Combining the Verlet and Cell Lists

F.4 Efficiency

G Reference States

G.1 Grand-Canonical Ensemble Simulation

H Statistical Mechanics of the Gibbs Ensemble

H.1 Free Energy of the Gibbs Ensemble

H.1.1 Basic Definitions

H.1.2 Free Energy Density

H.2 Chemical Potential in the Gibbs Ensemble

I Overlapping Distribution for Polymers

J Some General Purpose Algorithms

K Small Research Projects

K.1 Adsorption in Porous Media

K.2 Transport Properties in Liquids

K.3 Diffusion in a Porous Media

K.4 Multiple-Time-Step Integrators

K.5 Thermodynamic Integration

L Hints for Programming

Bibliography

Author Index

Index

前  言

Why did we write a second edition? A minor revision of the first edition would have been adequate to correct the (admittedly many) typographical mistakes. However, many of the nice comments that we received from students and colleagues alike, ended with a remark of the type: “unfortunately you don’t discuss topic x”. And indeed, we feel that, after only five years the simulation world has changed so much that the title of the book was no

longer covered by the contents. The first edition was written in 1995 and since then several new techniques have appeared or matured. Most (but not all) of the major changes in the second edition deal with these new developments. In particular, we have included a section on:

  • Transition path sampling and diffusive barrier crossing to simulate rare events
  • Dissipative particle dynamic as a course-grained simulation technique
  • Novel schemes to compute the long-ranged forces
  • Discussion on Hamiltonian and non-Hamiltonian dynamics in the context of constant-temperature and constant-pressure Molecular Dynamics simulations
  • Multiple-time-step algorithms as an alternative for constraints
  • Defects in solids
  • The pruned-enriched Rosenbluth sampling, recoil growth, and concerted rotations for complex molecules
  • Parallel tempering for glassy Hamiltonians

We have updated some of the examples to include also recent work. Several new Examples have been added to illustrate recent applications.

We have taught several courses on Molecular Simulation, based on the first edition of this book. As part of these courses, Dr. Thijs Vlugt prepared many Questions, Exercises, and Case Studies, most of which have been included in the present edition. Some additional exercises can be found on the Web. We are very grateful to Thijs Vlugt for the permission to reproduce this material.

Many of the advanced Molecular Dynamics techniques described in this book are derived using the Lagrangian or Hamilton formulations of classical mechanics. However, many chemistry and chemical engineering students are not familiar with these formalisms. While a full description of classical mechanics is clearly beyond the scope of the present book, we have added an Appendix that summarizes the necessary essentials of Lagrangian and Hamiltonian mechanics.

Special thanks are due to Giovanni Ciccotti, Rob Groot, Gavin Crooks, Thijs Vlugt, and Peter Bolhuis for their comments on parts of the text. In addition, we thank everyone who pointed out mistakes and typos, in particular Drs. J.B. Freund, R. Akkermans, and D. Moroni.

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