NANOCOMPUTING
Computational Physics for
NANOCOMPUTING
Computational Physics for
Nanoscience and Nanotechnology
James J Y Hsu
National Cheng Kung University, TaiwanNational Tsing Hua University, Taiwan
Published by
Pan Stanford Publishing Pte. Ltd. Penthouse Level, Suntec Tower 3 8 Temasek Boulevard
Singapore 038988
Email: [email protected] Web: www.panstanford.com
British Library Cataloguing-in-Publication Data
A catalogue record for this book is available from the British Library.
NANOCOMPUTING
Computational Physics for Nanoscience and Nanotechnology
Copyright © 2009 by Pan Stanford Publishing Pte. Ltd.
All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the Publisher.
For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher.
ISBN 978-981-4241-26-7 (Hardcover) ISBN 978-981-4241-27-4 (eBook)
RPS Nano Computing “preface” 2008/10/5 vii
PREFACE
The contents of this book are based on the material of Nano Com-puting course I taught at National Tsing Hua University since 2004. Nanotechnology is catching attention and gaining importance in both academia and industry alike, and students are very much interested in this emerging topic. There is the need to have a coherent presentation on the related disciplines, namely, theoretical physics, computer sci-ence, applied mathematics, and engineering study. In considering the importance of the four technologies for the future, Nano Technology (NT), Biomedical Technology (BT), Information Technology (IT), and Ecology Technology (ET), the course is designed to give breadth on related subjects, but keep depth on computation and physics.
On the theoretical side, we cover the Mesoscopic Physics and Nonlinear Many Body Physics. On the computer science, Object Ori-ented Programming and Parallel Computing are incorporated. On the applied mathematics, Asymptology and Algorithm are reviewed. For the engineering training, some applications and MATLAB are pre-sented. Students are introduced to the multiscales and multisciences from this book, and are requested to solve all the problems by either MATLAB or C++.
The target audience for the book is students at the senior and graduate level. The emphasis of this book is to teach students to solve problems from the features and characteristics of the problem itself, and not from a presumed methodology or a predefined tool. It tries
RPS Nano Computing “preface” 2008/10/5 viii
Preface
to avoid the students from falling into the mind frame of what the old saying, “If you are a hammer, everything else is a nail.” The rightful problem solving mentality is let the problem reveal where the solution might be, and study the clues to find the answers. Therefore, start from the asymptotic analysis once the problem is translated into a mathematical equation, and get all the hints possible even if a numerical solution is inevitable.
This book is organized as follows: It introduces the issues in nanoscience, reviews the mathematical tools both numerical and ana-lytical, and then applies the tools to more advanced problems through a repetition of the ideas and an increase in the level of sophistication so as to allow a deeper understanding of the physics and the prob-lem solving techniques. Finally, it applies the scientific knowledge for practical applications. The ultimate goal of this book is to pre-pare students with enough background to start working on a research dissertation in theoretical nanoscience.
James J. Y. Hsu March 2008
RPS Nano Computing “preface” 2008/10/5 v
ACKNOWLEDGEMENTS
I would like to thank Professor T. L. Lin for suggesting the course title, and ESS faculty and students for giving me the opportunity to teach this course. The interaction with Professor C. H. Tsai’s Car-bon Nanotube group was most beneficial. Many insightful help from colleagues, post-doctors and students at both NCKU and NTHU are gratefully acknowledged. Some derivations and programs were aided by Yee Mou Kao, Young-Chung Hsue, Chun Hung Lin, Eugene Pogorelov, Chieh-Wen Lo, Ying-Chi Chung, Chi-Yeh Chen, Robert Weng, Wellin Yang, Lichung Ko, and Cheng Hao Wu. This book was proofread by Dr. Fay Sheu. I also thank my wife, Dr. Yen-Hwa Hsu, and my daughters, Ingrid and Jessica, for their support to let me concentrate on research in Taiwan for the past few years.
This page intentionally left blank This page intentionally left blank
RPS Nano Computing “preface” 2008/10/5 ix
CONTENTS
Preface v Acknowledgement vii Chapter One Little Big Science 1
1.1 Tools for Measurement — To See is to Believe . . . 4
1.2 Carbon Tells Us First . . . 7
1.3 Mother Nature Knows Best . . . 10
1.4 Challenges in the New Millennium . . . 12
Chapter Two Tools for Analysis 19 2.1 MATLAB . . . 20
2.2 Program Control . . . 29
2.3 Asymptology . . . 33
Chapter Three Mesoscopic Systems 59 3.1 Review on Quantum Physics . . . 59
3.2 Quantum Chemistry . . . 78
3.3 Molecular Biology . . . 88
3.4 Condensed Matter Physics . . . 91
Chapter Four Analytical Chapter 115 4.1 Multiple Time Scales . . . 116
RPS Nano Computing “preface” 2008/10/5 x
Contents
Chapter Five Numerical Chapter 135
5.1 Recursion and Divide-and-Conquer . . . 136
5.2 Probabilistic Algorithm . . . 139
5.3 Evaluation and Search . . . 150
5.4 Molecular Dynamics . . . 159
5.5 Finite Element Method . . . 164
Chapter Six Nonlinear Many Body Physics and Transport 187 6.1 Density Functional Theory . . . 189
6.2 Correlation and Coherence . . . 199
6.3 Green’s Function Method . . . 204
6.4 Transport . . . 218
Chapter Seven OOP, MPI and Parallel Computing 227 7.1 C++ and Object Oriented Programming . . . 228
7.2 Message Passing Interface . . . 233
7.3 OpenMP . . . 242
Chapter Eight Low Dimensionality and Nanostructures 245 8.1 Quantum Dot and Quantum Wire . . . 245
8.2 Nanostructure Electronic Properties . . . 252
Chapter Nine Special Topics 261 9.1 Plasmon . . . 261
9.2 Quantum Hall Effect . . . 277
9.3 Chaos and Stochasticity . . . 284
RPS Nano Computing “preface” 2008/10/5 xi
Contents
Chapter Ten Applications 303
10.1 Carbon Nanotube . . . 303 10.2 Water Dynamics . . . 314 10.3 Molecular Computer . . . 324 References 333 Function Index 345 Author Index 349 Keyword Index 353 Nano Computing xi
This page intentionally left blank This page intentionally left blank