The Art of Molecular Dynamics Simulation

Book Description

In this Second Edition an extensive series of detailed case studies introduces the reader to solutions to a variety of problems connected with the way molecular interactions and motions determine the properties of matter. The methods are widely used in studying phenomena involving everything from the simplest of liquids to highly complex molecules such as proteins. In addition to a significant amount of new material, this edition features completely rewritten software. First Edition Hb (1996): 0-521-44561-2 First Edition Pb (1996): 0-521-59942-3

Customer Reviews:

Useful, for the right reader.......2005-05-10

I'm not sure I'm that reader.

The ideal reader is wholly at home with good bits of analysis - you'll be comfortable with Lagrange multipliers, LU decomposition, quaternion representation of oriented values, and a fair bit else. You won't need the basics of classical physics, including Hamiltonians and a few projections of the Navier-Stokes equations down into tractable form. Non- and in-equilibrium dynamics, smooth and discrete representations, plus their mixed forms - you're prepared to build up from these elements.

You, the ideal reader, are not much of a programmer, though. The book built very much around extensive C sample code. I use the term "C" in some strict syntactic sense, though. The general style reminds me of FORTRAN, but the global data declarations are in the style of pre-1980 BASIC. This book is aimed at the odd mix of capable numerical analyst (which I'm not) and chemist (which I'm not), but naive software developer (which I'm not).

The strength of this book is in its code samples. The author explictly invites modification and extension. The only sane way to modify this code is to understand it thoroughly, and to understand the underlying chemistry, physics, and numerical models.

Maybe this book works well for some people, people that I admire immensely. I just wish it worked better for me.

//wiredweird

Too much and too little........2002-05-30

This book is in some ways a reasonable introduction to MD. It's the only book I know that actually shows the derivatives of energy functions necessary for writing efficient MD code. Unfortunately it does so in a hard to follow way. This is typical of the rest of the text. The example C code is hideous both in format and style. Missing from the book are essential formulae for calculating macroscopic properties from MD simulations. It is probably the best practical guide to writing MD code, but that isn't saying much.

A good introduction to Molecular Dynamics.......2001-08-30

This book constitutes a good introduction to the methods of Molecular Dynamics. Besides clear descriptions of the methods and algorithms, it includes C example implementations commented on the book to illustrate the points. It is almost an introducory 'recipe' book. For advanced tips, Frenkel-Smit will give good lead, but at the cost of less readability and Fortran (pseudo)code.
Certainly, the underlying philosophy of the code may seem awkward initially, but it is not a matter of "C design", rather of coding philosophy and program design. Once you get to understand it, it becomes easy and "natural". And what's even more important: it reflects the program design philosophy in use in the Molecular Modelling field, hence getting used to it will help you understand most existing production code.
The electronic version of the C code (available at the book's web site) is a mesh though: it lacks comments and makes heavy use of conditional compilation to render the examples from a single, convoluted source. The ingenious programmer won't be misled by this however: a simple step with the C preprocessor will distil the actual code. Not to mean it is not inconvenient anyway (sic). Certainly, it would have been a lot better if the authors had separated, cleaned and commented the code for the examples in the electronic version.
Besides, the book comes with additional, not too difficult programming assignments that make for extra fun and deeper understanding.
Once you are done with this book, you'll be in a position to really appreciate and use Frenkel-Smit and other advanced texts.

Good book on subject, needs a REAL C second edition.......2000-08-05

This is a good and honest book on the subject, it needs a second edition in pure C language and not the 'f2c-like' used. Many techiques like linked lists are simple and clear in C but confuse when translated to Fortran (77 or the new 90/95 variants)

Excellent introduction to MD simulation.......2000-03-25

Strengths: Excellent selection of topics, with good references and enough discussion of the underlying scientific theory. Thoughtful and well-written. DO NOT USE MERELY AS A COOKBOOK!

Weaknesses: Antiquated code, basically FORTRAN with a C veneer. Although the code works as is and is blazingly fast, it's not usable as a basis for further code development -- readers will want to recast the ideas and algorithms in their own up-to-date C code. For example, his arrays start at 1; the only data structure is the array (ugh!), there are no structures. Things get hard to understand when he starts packing multiple array indices into a single composite index, then unpacks it (see, e.g., the code on autocorrelation functions, Chap. 5).

However, the awkward code is a blessing in disguise -- write your own and you'll learn an incredible amount! This book gives you all the conceptual tools to do this, and you can use the code supplied (available from the publisher) as a benchmark and check. Actually, there are a few bugs in the code, but considering its complexity (much of which is unavoidable), it is remarkably reliable. In general, the code is optimized for efficiency, not for ease of maintenance or generalization.

Book Description

Electronic structure problems are studied in condensed matter physics and theoretical chemistry to provide important insights into the properties of matter. This graduate textbook describes the main theoretical approaches and computational techniques, from the simplest approximations to the most sophisticated methods. It starts with a detailed description of the various theoretical approaches to calculating the electronic structure of solids and molecules, including density-functional theory and chemical methods based on Hartree-Fock theory. The basic approximations are thoroughly discussed, and an in-depth overview of recent advances and alternative approaches in DFT is given. The second part discusses the different practical methods used to solve the electronic structure problem computationally, for both DFT and Hartree-Fock approaches. Adopting a unique and open approach, this textbook is aimed at graduate students in physics and chemistry, and is intended to improve communication between these communities. It also serves as a reference for researchers entering the field.

Introduction to Device Modeling and Circuit Simulation

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Introduction to Device Modeling and Circuit Simulation
Tor A. Fjeldly , Trond Ytterdal , and Michael S. Shur
Manufacturer: Wiley-Interscience
ProductGroup: Book
Binding: Hardcover

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ASIN: 0471157783

Book Description

This book is a useful reference for practicing electrical engineers as well as a textbook for a junior/senior or graduate level course in electrical engineering. The authors combine two subjects: device modeling and circuit simulation - by providing a large number of well-prepared examples of circuit simulations immediately following the description of many device models.

Nanoscale Phase Separation and Colossal Magnetoresistance

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Nanoscale Phase Separation and Colossal Magnetoresistance
Elbio Dagotto
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 3540432450

Book Description

The study of the spontaneous formation of nanostructures in single crystals is rapidly developing into a dominant field of research in the subject area known as strongly correlated electrons. The structures appear to originate in the competition of phases. This book addresses nanoscale phase separation, focusing on the manganese oxides with colossal magnetoresistance (CMR). The text argues that nanostructures are at the heart of the CMR phenomenon. Other compounds are also addressed, such as high-temperature superconductors, where similar nanostructures exist. Brief contributions by distinguished researchers are also included. The book contains updated information directed at experts, both theorists and experimentalists. Beginning graduate students or postdocs will also benefit from the introductory material of the early chapters, and the book can be used as a reference for an advanced graduate course.

Interatomic Forces in Condensed Matter (Oxford Series on Materials Modelling, 1)

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Great content but could be written in a simpler manner

Interatomic Forces in Condensed Matter (Oxford Series on Materials Modelling, 1)
Mike Finnis
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Hardcover

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ASIN: 0198509774

Book Description

There is a continuing growth of interest in the computer simulation of materials at the atomic scale, using a variety of academic and commercial computer programs. In all such programs there is some physical model of the inter-atomic forces, which may be based on something as simple as a pair interaction, such as the Lennard-Jones model, or as complex as a self-consistent, all-electron solution of the quantum mechanical problem. For a student or researcher, the basis of such models is often shrouded in mystery. It is usually unclear how well founded they are, since it is hard to find a discussion of the physical assumptions that have been made in their construction. The lack of clear understanding of the scope and limitations of a given model may lead to its innocent misuse, resulting either in unfair criticism of the model or in the dissemination of nonsensical results. In the present book, models of inter-atomic forces are derived from a common physical basis, namely the density functional theory. The interested reader will be able to follow the detailed derivation of pairwise potentials in simple metals, tight-binding models from the simplest to the most sophisticated (self-consistent) kind, and various ionic models. The book is self-contained, requiring no more background than provided by an undergraduate quantum mechanics course. It aims to furnish the reader with a critical appreciation of the broad range of models in current use, and to provide the tools for understanding other variants that are described in the literature. Some of the material is new, and some pointers are given to possible future avenues of model development.

Customer Reviews:

Great content but could be written in a simpler manner.......2004-06-22

I read this book as preparation for my Ph.D. comprehensive exams. Specifically, I wanted to improve my understanding of materials modelling and density functional theory. This book did accomplish this. It provides a very comprehensive study of how interatomic forces are calculated in solids. Density functional theory, tight binding, empirical potentials, linear response theory, phonon calculation, and elastic constants were all here.

The focus was tight; with minimal straying into related topics such as electronic structure, Monte Carlo, or modelling of gases or liquids. As such, this book is great for materials engineers and scientists, but is useless for chemists and probably most physicists.

The book leans towards the theoretical side; minimal discussion of how the different equations would be implemented into code. Hence don't use this book as a guide to writing a simulation software. But do use it as a guide to understanding how to use a simulation software to obtain results. Suprisingly, the text does not require a lot of prior knowledge in thermodynamics, crystallography, quantum, or solid state; thereby making it more readable for people from a wide range of technical backgrounds.

Book Description

Paperback. This book is a collection of key reprints of papers on the computer simulation of statistical-mechanical systems, introduced and commented upon by the editors.

The papers presented here provide the reader with a complete and comprehensive source book. It enables the new and experienced practitioner of computer simulation to learn and use the various methods and interpret the restrictions and various possibilities.

Book Description

This new and exciting interactive resource package centers around fourteen high quality computer simulations covering essential topics in solid state physics. The computer simulations provided on CDSHROM cover x-ray diffraction, phonons, electron states and dynamics, semiconductors, magnetism, and dislocations. Users can vary different characteristics and immediately see the results in animations and graphical displays. The companion book is essential for effective use of the simulations. It guides the user through hundreds of exercises and examples, illustrates fundamental physical principles, and contains notes on the relevant physics. The hardcover edition includes the simulations on CDSHROM (Unix, Windows, Powermac formats) and a license for use on a local area network on a single geographical site. The low priced paperback (without CDSHROM) is intended for students who have access to the simulations on a local area network. These simulations provide an interactive resource for those studying solid state physics at advanced undergraduate or graduate level. They will also be of interest to researchers in physics, materials science, electrical engineering, chemistry and chemical engineering. Selected material from the simulations may be explored at the Web site http://www.ruph.cornell.edu/sss/sss.html after February 1, 1997.

Customer Reviews:

Waste of money.......2006-01-21

Every student I have spoken to who has been required to use these simulations and the book in their Solid State course regard this book to be the waste of your time and money.

First of all, the book does not explain theory, all you have to do is to run the simulations and complete the exercises. The Package contains 14 separate programs that you run. Each program corresponds to a particular theory in Solid State physics, like Drude theory, for example. This book basically explains how the computer simulations work and has a considerable number of Exercises to accomplish with the use of the simulation programs.

When you run the simulations it seems like you are making an experiment because the data you get has a certain random error associated with it. So, basically you can control some input parameters and you observe the result calculated on the basis of a certain theoretical algorithm.

Very often the Exercises ask you to compare the data you obtain running the simulations with a certain theoretical formula. This way the authors basically ask you to compare the model they used in the simulation with the theory. That is in most exercises you do nothing more but simply make sure that the algorithms in the programs comply with the theory, you make sure they do work. You don't really study physics this way; the simulations do very little in helping you understand. Unfortunately, these simulations are only good for undergraduate students with very little knowledge of physics. I would say the package is designed for theoreticians who would like to feel what it is like to perform an experiment not for explaining solid state.

I am surprised Cambridge University Press would publish a book like that. If you really want to learn Solid State it is better to spend this money on purchasing something which will help you learn the subject.

Buy the soft-cover book instead.......2004-02-17

The hardcover version of this book which includes the CD-ROM with all of the simulations is no longer in print. Check out the book's website at http://www.ruph.cornell.edu/sss/sss.html and you should be able to download the computer simulations for free (at least as of February 2004.) The paperback book is a very helpful companion to these programs and includes lots of useful exercises as well as concise summaries of the basic concepts of solid state physics without getting lost in mathematical derivations like most textbooks seem to do.

You don't need the CD-ROM.......2004-02-17

The hardcover version of this book which includes the CD-ROM with all of the simulations is no longer in print. Check out the book's website at http://www.ruph.cornell.edu/sss/sss.html and you should be able to download the computer simulations for free (at least as of February 2004.) This paperback book is a very helpful companion to these programs and includes lots of useful exercises as well as concise summaries of the basic concepts of solid state physics without getting lost in mathematical derivations like most textbooks seem to do.

Note on CD.......2000-07-19

This is not a review. In case anyone misses it the CD with the simulations is only available with the hard cover version of this book. Be aware of this when you make a choice to buy the book.

Excellent collection of computer simulations.......1999-09-24

This is an excellent collection of solid state physics computer simulations that I recommend highly.

Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 (Lecture Notes in Physics)

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Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 (Lecture Notes in Physics)

Manufacturer: Springer
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Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 2 (Lecture Notes in Physics)

ASIN: 3540352708

Book Description

This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. It will enable the graduate student and both the specialist and nonspecialist researcher to get acquainted with the tools necessary to carry out numerical simulations at an advanced level. Volume 2 published as LNP 704 (ISBN 3-540-35283-X) is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology.

Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 2 (Lecture Notes in Physics)

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Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 2 (Lecture Notes in Physics)

Manufacturer: Springer
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Binding: Hardcover

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Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1 (Lecture Notes in Physics)

ASIN: 354035283X

Book Description

This extensive and comprehensive collection of lectures by world-leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1, published as LNP 703 (ISBN 3-540-35270-8) is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. It will enable the graduate student and both the specialist and nonspecialist researcher to get acquainted with the tools necessary to carry out numerical simulations at an advanced level. The present volume is a state-of-the-art survey on numerical experiments carried out for a great number of systems, ranging from materials sciences to chemical biology, such as supercooled liquids, spin glasses, colloids, polymers, liquid crystals, biological membranes and folding proteins.

1st Italian Conference on Sensors and Microsystems

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1st Italian Conference on Sensors and Microsystems
A. D'Amico , and C. Di Natale
Manufacturer: World Scientific Publishing Company
ProductGroup: Book
Binding: Hardcover

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