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1. computer simulation of liquid

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2. The Art of Molecular Dynamics Simulation

ÎļþÃû:D C Rapaport---The Art of Molecular Dynamics Simulation.pdf

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¡¾×÷Õß¡¿Dennis C Rapaport

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     This book describes the extremely powerful technique of molecular dynamics simulation, which involves solving the classical many-body problem in contexts relevant to the study of matter at the atomic level. The method allows the prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules. Because there is no alternative approach capable of handling such a broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This volume will be of value to advanced students and researchers in physics, chemistry, polymer science and materials science in universities and industrial laboratories.

Contents
Preface

1 Introduction

2 Basic MD approach
soft-disk fluid, methodology, programming, equilibration, sample results.

3 Simulating simple systems
equations of motion, potential functions, interaction computations, integration methods, initial state, efficiency, trajectory sensitivity.

4 Equilibrium properties of simple fluids
thermodynamics, structure, Voronoi polyhedra, clusters.

5 Dynamical properties of simple fluids
transport coefficients, space-time correlation functions.

6 Alternative ensembles
feedback and constraint methods for constant temperature and pressure.

7 Nonequilibrium dynamics
homogeneous and inhomogeneous systems, sheared flow, heat transport.

8 Rigid molecules
dynamics, molecular construction, water, properties, hydrogen bonds.

9 Flexible molecules
polymer chains, properties.

10 Geometrically constrained molecules
solving the constraint problem, internal forces, alkane chains, properties.

11 Other interactions
long-range forces, three-body potentials, dipole fluid, liquid silicon.

12 Step potentials
computational scheme, events, results, generalizations.

13 Time-dependent phenomena
open systems, thermal convection, obstructed flow.

14 Algorithms for supercomputers
MD algorithms for distributed- and vector-processing computers.

15 The future

Appendices
data management, organizing extensive computations, utility functions, list of variables.

Bibliography

Indices
function index, subject index.

[ Last edited by lei0736 on 2008-3-9 at 22:12 ]
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3. Introduction to Modeling and Simulation½²Òå

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4. Understanding Molecular Simulation From Algorithms to Applications

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D.Frenkel---Understanding Molecular Simulation From Algorithms to Applications.rar
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ISBN: 0122673700
Title: Understanding Molecular Simulation: From Algorithms to Applications 1996-08
Author: Daan Frenkel, Berend Smit
Publisher: Academic Press
Publication Date: 1996-08
Number Of Pages: 443
Average Amazon Rating: 4.5
Summary:
Computer simulation techniques have become almost essential in the study of the macro-molecular phenomena and phase behavior on the molecular level. As these techniques become increasingly important, it is necessaryto realize that they are useful tools, but are not the goals of research. With this important distinction in mind, Understanding Molecular Simulation describes simulation techniques along with the physics behind the phenomena that these techniques simulate.
Each chapter is comprised of three components: the general theoretical basis, an outline of the necessary computer code, and a few applications which illustrate the use of the technique demonstrated. The chapters also include examples of the typical practical problems that could be solved using each technique.

Key Features
* Gives a unified presentation of computational tools used to study molecular systems in the equilibrium state
* Describes simulation techniques and physics behind the phenomena simulated
* Emphasizes important topics of phase behavior and computer simulation of macro-molecular (polymer-type) substances
* Includes references to the authors home page where additional information from the authors can be found


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4Â¥2008-03-05 21:41:41
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5. Statistical Mechanics - Algorithms and Computations

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Statistical Mechanics - Algorithms and Computations, Krauth, Oxford 2006.pdf

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Description
This book discusses the computational approach in modern statistical physics in a clear and accessible way and demonstrates its close relation to other approaches in theoretical physics. Individual chapters focus on subjects as diverse as the hard sphere liquid, classical spin models, single quantum particles and Bose-Einstein condensation. Contained within the chapters are in-depth discussions of algorithms, ranging from basic enumeration methods to modern Monte Carlo techniques. The emphasis is on orientation, with discussion of implementation details kept to a minimum. Illustrations, tables and concise printed algorithms convey key information, making the material very accessible. The book is completely self-contained and graphs and tables can readily be reproduced, requiring minimal computer code. Most sections begin at an elementary level and lead on to the rich and difficult problems of contemporary computational and statistical physics. The book will be of interest to a wide range of students, teachers and researchers in physics and the neighbouring sciences. An accompanying CD allows incorporation of the book's content (illustrations, tables, schematic programs) into the reader's own presentations.
Reviews
"This book is the best one I have reviewed all year."-- Physical Sciences Educational Reviews

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5Â¥2008-03-05 21:47:35
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6. A practical guide to computer simulations

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A. K. Hartmann---A practical guide to computer simulations.pdf

Here practical aspects of conducting research via computer simulations
are discussed. The following issues are addressed: software engineering,
object-oriented software development, programming style, macros, make
files, scripts, libraries, random numbers, testing, debugging, data plotting,
curve fitting, finite-size scaling, information retrieval, and preparing
presentations.

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7. Molecular Modelling Principles and Applications

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A.R.Leach---Molecular Modelling Principles and Applications.pdf

This book provides a detailed description of the techniques employed in molecular modelling and computational chemistry. The first part of the book covers the two major methods used to describe the interactions within a system (quantum mechanics and molecular mechanics). The second part then deals with techniques that use such energy models, including energy minimisation, molecular dynamics, Monte Carlo simulations and conformational analysis. The author also discusses the use of more advanced modelling techniques such as the calculation of free energies and the simulation of chemical reactions. In addition he considers aspects of both chemoinformatics and bioinformatics and techniques that can be used to design new molecules with specific properties. Many of the topics are treated in considerable depth but the reader is assumed to have but a basic knowledge of the relevant physical and chemical principles.
Most of the theoretical sections are accompanied by simple calculations together with examples drawn from the literature. The book is well illustrated and a colour plate section highlights the impact of computer molecular graphics. The book will prove a valuable text for postgraduate students and professionals and many sections will be useful to final-year undergraduates taking courses in molecular modelling or computational chemistry.


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7Â¥2008-03-05 22:05:56
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8. An Introduction to Computer Simulation

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Computer simulation is increasingly used in physics and engineering to predict the probable outcome of experiments and to aid in their interpretation. The methods of simulation are based on a range of numerical techniques for treating ordinary and partial differential equations. Since much of physics can be broken down into a relatively small set of fundamental equations, there is a set of very general methods which can be widely applied. This text aims to give an introduction to those methods suitable for readers at an undergraduate level and those meeting the subject for the first time at postgraduate level. The methods are illustrated with simple programs and problems. The book covers a range of material not available in a simple form in a single text elsewhere.

Table of Contents

List of programs available
1 Models and simulation 1
2 Finite-difference methods 33
3 Simulation with particles 87
4 The Monte Carlo method 129
5 The wave equation 156
6 The finite-element method 179
7 Computational fluid dynamics 211
App. 1 The elements of matrix algebra 259
App. 2 A simple conjugate gradient method 265
App. 3 The virial theorem 268
App. 4 The condition for collisionless PIC 270
App. 5 The coefficients of a half-sine-wave Fourier series 273
App. 6 Numerical quadrature 274
App. 7 Calculation of the four-element solution to (6.11) 284
Problems - solutions and comments 287
References 307
Index 309

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9. MIT 2005 Atomistic Computer Modeling of Materials

ÎļþÃû£ºAtomistic Computer Modeling of Materials .pdf

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¼ò½é£ºThis course uses the theory and application of atomistic computer simulations to model, understand, and predict the properties of real materials. Specific topics include: energy models from classical potentials to first-principles approaches; density functional theory and the total-energy pseudopotential method; errors and accuracy of quantitative predictions: thermodynamic ensembles, Monte Carlo sampling and molecular dynamics simulations; free energy and phase transitions; fluctuations and transport properties; and coarse-graining approaches and mesoscale models. The course employs case studies from industrial applications of advanced materials to nanotechnology. Several laboratories will give students direct experience with simulations of classical force fields, electronic-structure approaches, molecular dynamics, and Monte Carlo

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9Â¥2008-03-05 22:17:30
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10. Molecular hydrodynamics

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Boon, Yip. Molecular hydrodynamics (Dover, 1991)(T)(ISBN 0486669491)(429s)_PT_.djvu

Molecular Hydrodynamics

Title: Molecular Hydrodynamics
Author: Jean Pierre Boon Sidney Yip
Publisher: Dover Publications
Publication Date: 1992-01-14
Number Of Pages: 432


This graduate-level introduction to the theory and applications of time correlation functions and the molecular theory of fluid dynamics provides experimentalists with the theoretical tools useful for analysis of experimental results, and theoreticians a comprehensive source of illustrations of theories most relevant in practical applications. The book reviews the concepts, basic tools and basic approximations of molecular hydrodynamics, then explores self-diffusion, space-dependent diffusion,



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10Â¥2008-03-05 22:22:01
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11. Computational chemistry-A Practical Guide for Applying Techniques to RealWorld Problems

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Computational chemistry-A Practical Guide for Applying Techniques to RealWorld Problems(wiley2001).pdf

Young, David C. \"Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems\"
ISBN: 0471333689 | John Wiley & Sons, 2001 | pdf | 370 pgs | 1.50 Mb

A practical, easily accessible guide for bench-top chemists, this book focuses on accurately applying computational chemistry techniques to everyday chemistry problems. Provides nonmathematical explanations of advanced topics in computational chemistry.

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12. Computational Materials Chemistry_Methods and Applications

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Computational Materials Chemistry_Methods and Applications_1402017677.pdf

Computational Materials Chemistry: Methods and Applications

ISBN: 1402017677
Title: Computational Materials Chemistry: Methods and Applications
Author: L.A. Curtiss (Editor), M.S. Gordon (Editor)
Publisher: Springer
Publication Date: 2004-05-26
Number Of Pages: 380

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very good! thank you a lot.
14Â¥2008-03-06 20:07:50
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anyway, very good! thank you a lot.
16Â¥2008-03-06 22:09:44
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13. Computational Nanomechanics of Materials

ÎļþÃû£ºComputational Nanomechanics of Materials.pdf

Handbook of Theoretical and Computational NanotechnologyµÄÒ»²¿·Ö ¿ÉÒÔ¶ÀÁ¢³ÉÕÂ

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14. Computational Simulation of Materials

ÎļþÃû£ºcomputational simulation of materials-notes for lectures given at UCSB.pdf

This report presents information from a lecture given on the computational simulation of materials. The purpose is to introduce modern computerized simulation methods for materials properties and response.



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19Â¥2008-03-07 21:05:57
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11. Computational chemistry-A Practical Guide for Applying Techniques to RealWorld Problems

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15. Computer Modeling in Inorganic Crystallography

By C.R.A. Catlow

--------------------------------------------------------------------------------



Publisher: Academic Press
Number Of Pages: 340
Publication Date: 1997-02-17
ISBN-10 / ASIN: 012164135X
ISBN-13 / EAN: 9780121641351
Binding: Hardcover


--------------------------------------------------------------------------------

Book Description:

Computer simulation techniques are now having a major impact on almost all areas of the physical and biological sciences. This book concentrates on the application of these methods to inorganic materials, including topical and industrially relevant systems including zeolites and high Tc superconductors.
The central theme of the book is the use of modern simulation techniques as a structural tool in solid state science. Computer Modelling in Inorganic Crystallography describes the current range of techniques used in modeling crystal structures, and strong emphasis is given to the use of modeling in predicting new crystal structures and refining partially known structures. It also reviews new opportunities being opened up by electronic structure calculation and explains the ways in which these techniques are illuminating our knowledge of bonding in solids.

Key Features
* Includes a thorough review of the technical basis of relevant contemporary methodologies including minimization, Monte-Carlo, molecular dynamics, simulated annealing methods, and electronic structure methods
* Highlights applicati** to amorphous and crystalline solids
* Surveys simulati** of surface and defect properties of solids
* Discusses applicati** to molecular and inorganic solids

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29Â¥2008-03-11 12:49:55
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16. Computer Modelling of Microporous Materials

B. SmitµÄ´ó×÷

By: C.R.A. Catlow(Editor) R.A. van Santen(Editor) B. Smit(Editor)
ISBN: 0121641376
Publisher: Academic Press - 2004-06-11
Hardcover | 298 Pages | List Price: $153.00 (USD)

Microporous materials, including both zeolites and aluminophosphates are amongst the most fascinating classes of materials, with wide ranging important applications in catalysis, gas separation and ion exchange. The breadth of the field has, moreover, been extended in the last ten years by the discovery of the versatile and exciting ranges of mesoporous materials. Computational methods have a long and successful history of application in solid state and materials science, where they are indeed established tools in modelling structural and dynamic properties of the bulk and surfaces of solids; and where they are playing an increasingly important role in understanding reactivity. Their application to zeolite science developed strongly in the 1980's, with the initial successes in modelling structure and sorption, and with emerging capability in quantum mechanical methods. The field was reviewed over ten years, since then there have been major developments in techniques and of course the power of the available hardware, which have promoted a whole range of new applications to real complex problems in the science of microporous materials. This book aims to summarise and illustrate the current capabilities of atomistic computer modelling methods in this growing field.

Audience
Chemical engineers, geologists, theoretical chemists, physical chemists, material scientists, in academia and industry.

Contents
1.Static Lattice Modelling and Structure Prediction of Micro- and Meso-Porous Materials 2.Adsorption Phenomena in Microporous Materials 3.Dynamics of Sorbed Molecules in Zeolites 4.Monte Carlo Simulations of Diffusion and Reactions in Zeolites 5.Plane Wave Pseudopotential Modelling Studies of Zeolites 6.Reaction Mechanisms in Solid Acid Catalysts 7.Structure and Reactivity of Metal Ion Species in High Silica Zeolites 8.Template Host Interaction and Template Design 9.The Interplay of Experiment and Simulation in Zeolite Science

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17. Computer Simulation of Materials at Atomic Level

Review
"A compilation of 34 papers from the workshops First-Principles, Tight-Binding, and Empirical Methods for Materials Simulation and Massively Parallel and Superscalar Applications in Computational Materials Science." (SciTech Book News, Vol. 25, No. 4, December 2001)

Book Description
Combining theory and applications, this book deals with the modelling of materials properties and phenomena at atomic level.
The first part provides an overview of the state of the art of computational solid state physics. Emphasis is given on the understanding of approximations and their consequences regarding the accuracy of the results. This part of the book also deals as a guide to find the best method for a given purpose.
The second part offers a potpourri of interesting topical applications, showing what can be achieved by computational modelling. Here the possibilities and the limits of the methods are stressed.

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31Â¥2008-03-11 12:57:33
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18. Computer Simulations of Dislocations (Oxford Series on Materials Modelling)
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by Vasily Bulatov, Wei Cai

Book Description
This book presents a broad collection of models and computational methods - from atomistic to continuum - applied to crystal dislocations. Its purpose is to help students and researchers in computational materials sciences to acquire practical knowledge of relevant simulation methods.
Because their behavior spans multiple length and time scales, crystal dislocations present a common ground for an in-depth discussion of a variety of computational approaches, including their relative strengths, weaknesses and inter-connections. The details of the covered methods are presented in
the form of "numerical recipes" and illustrated by case studies. A suite of simulation codes and data files is made available on the book's website to help the reader "to learn-by-doing" through solving the exercise problems offered in the book.

Hardcover: 304 pages
Publisher: Oxford University Press, USA (December 11, 2006)
Language: English
ISBN-10: 0198526148
ISBN-13: 978-0198526148

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19. D.P.Landou- K.Bind---A Guide to Monte Carlo Simulations in Statistical Physics, 2nd Edition

A Guide to Monte Carlo Simulations in Statistical Physics, Second Edition
Cambridge University Press | 2005 | 448 pages | ISBN-10: 0521842387 | 3.70 MB | PDF

This new and updated edition deals with all aspects of Monte Carlo simulation of complex physical systems encountered in condensed-matter physics, statistical mechanics, and related fields. After briefly recalling essential background in statistical mechanics and probability theory, it gives a succinct overview of simple sampling methods. The concepts behind the simulation algorithms are explained comprehensively, as are the techniques for efficient evaluation of system configurations generated by simulation. It contains many applications, examples, and exercises to help the reader and provides many new references to more specialized literature. This edition includes a brief overview of other methods of computer simulation and an outlook for the use of Monte Carlo simulations in disciplines beyond physics. This is an excellent guide for graduate students and researchers who use computer simulations in their research. It can be used as a textbook for graduate courses on computer simulations in physics and related disciplines.

ÏàÐÅ D.P.Landou ºÍK.Binder ÕâÁ½¸öÈ˵ÄÃû×Ö¶Ô×öMCµÄÀ´Ëµ²»Ä°Éú°É

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20. D.Raabe---Computational Materials Science

Modeling and simulation play an ever increasing role in the development and optimization of materials.
Computational Materials Science presents the most important approaches in this new interdisciplinary field of materials science and engineering. The reader will learn to assess which numerical method is appropriate for performing simulations at the various microstructural levels and how they can be coupled.
This book addresses graduate students and professionals in materials science and engineering as well as materials-oriented physicists and mechanical engineers.


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21. Delerue & Lannoo, Nanostructures - Theory and Modelling

Publisher:   Springer
Number Of Pages:   304
Publication Date:   2004-03-31
Sales Rank:   1058649
ISBN / ASIN:   3540206949
EAN:   9783540206941
Binding:   Hardcover
Manufacturer:   Springer
Studio:   Springer




Progress in nanoscience is becoming increasingly dependent on simulation and modelling. This is due to a combination of three factors: the reduced size of nano-objects, the increasing power of computers, and the development of new theoretical methods. This book represents the first attempt to provide the theoretical background needed by physicists, engineers and students to simulate nanodevices, semiconductor quantum dots and molecular devices. It presents in a unified way the theoretical concepts, the more recent semi-empirical and ab-initio methods, and their application to experiments. The topics include quantum confinement, dielectric and optical properties, non-radiative processes, defects and impurities, and quantum transport. This guidebook not only provides newcomers with an accessible overview (requiring only basic knowledge of quantum mechanics and solid-state physics) but also provides active researchers with practical simulation tools


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37Â¥2008-03-15 14:55:30
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22. Furio Ercolessi---A molecular dynamics primer


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23.Principles Of Nanotechnology  Molecular-Based Study Of Condensed Matter In Small Systems

Publisher: World Scientific Publishing Company
  
This invaluable book provides a pointed introduction to the fascinating subject of bottom-up nanotechnology with emphasis on the molecular-based study of condensed matter in small systems. Nanotechnology has its roots in the landmark lecture delivered by the famous Nobel Laureate physicist, Richard Feynman, on 29 December 1959 entitled "There's Plenty of Room at the Bottom." By the mid-1980s, it had gained real momentum with the invention of scanning probe microscopes. Today, nanotechnology promises to have a revolutionary impact on the way things are designed and manufactured in the future.
Principles of Nanotechnology is self-contained and unified in presentation. It may be used as a textbook by graduate students and even ambitious undergraduates in engineering, and the biological and physical sciences who already have some familiarity with quantum and statistical mechanics. It is also suitable for experts in related fields who require an overview of the fundamental topics in nanotechnology. The explanations in the book are detailed enough to capture the interest of the curious reader, and complete enough to provide the necessary background material needed to go further into the subject and explore the research literature. Due to the interdisciplinary nature of nanotechnology, a comprehensive glossary is included detailing abbreviations, chemical formulae, concepts, definitions, equations and theories

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24. Dynamics of Molecule Surface Interaction

Title: Dynamics of Molecule Surface Interaction 1999-12
Author: Gert Due Billing
Publisher: Wiley-Interscience
Publication Date: 1999-12-20
Number Of Pages: 235

Book Description
Chemical reactions at surfaces do not follow the same reaction dynamics as atoms in the gas phase. The changes from "ideal" interactions depend on the electronic structure and the spatial and geometric shape of the surface. The dynamics of chemical reactions at surfaces have all the complexity of gas-phase molecules reaction dynamics, plus those associated with the additional phenomena due to the presence of a solid surface.

Book Info
A chemist's point of view of the dynamics of molecule surface interactions, requiring some understanding of the properties and physics of solids. Contains the most important research results in this area, taking a microscopic molecular dynamics point of view rather than a macroscopic kinetic point of view. A graduate level textbook. DLC: Gas-solid interfaces.

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25. H. S. Park---Nano Mechanics and Materials

Wing Kam Liu / Eduard G. Karpov / Harold S. Park, Nano Mechanics and Materials: Theory, Multiscale Methods and Applications
Wiley | ISBN 0470018518 | 2006-03-13 | PDF | 5 Mb | 334 pages

Book Description:

Nanotechnology is a progressive research and development topic with large amounts of venture capital and government funding being invested worldwide. Nano mechanics, in particular, is the study and characterization of the mechanical behaviour of individual atoms, systems and structures in response to various types of forces and loading conditions.

This text, written by respected researchers in the field, informs researchers and practitioners about the fundamental concepts in nano mechanics and materials, focusing on their modelling via multiple scale methods and techniques. The book systematically covers the theory behind multi-particle and nanoscale systems, introduces multiple scale methods, and finally looks at contemporary applications in nano-structured and bio-inspired materials.

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