The first edition of this text was published in 2006, and much in the world and our lives has changed. We are still eternally grateful for the support and encouragement of our colleagues and students, but we have also had enormously important input from many external users of the book. The development of the second edition has been no less a labor of love than the first, but we have written it with significantly more experience professionally. Colleagues at Wofford College have been especially accommodating in their willingness to class-test many of the new modules and to provide us with extraordinarily constructive suggestions for improvement. In particular, we would like to thank Drs. Anne J. Catllá, Joseph D. Sloan, and David A. Sykes. Drs. Catllá and Sloan used the first edition and new materials in their modeling and simulation classes, and Dr. Sykes meticulously reviewed most of the new modules and projects. Drs. Ted Monroe and Joseph Spivey also gave very helpful feedback on several of the new modules they utilized in their upper-level mathematics courses.
We are privileged to teach in an institution that attracts an extraordinarily talented group of science, computer science, and mathematics students, several of whom have contributed directly and indirectly to the development of various modules and associate files. We would like to recognize particularly Mayfield Reynolds, Shay Ellison, Jesse Hanley, and Whitney Sanders for their dedication, creativity, and diligence.
Additionally, we would like to acknowledge the generous comments and contributions from Dr. Stephen Davies, computer scientist at Mary Washington University. Dr. Davies has not only shared excellent feedback for the first edition, but he also has contributed directly to this edition by allowing us to incorporate an interesting module he developed (Module 7.6 “Plotting the Future: How Will Your Garden Grow”) and a clever Project 10 on paratroopers in Module 3.1, “Modeling Falling and Skydiving.”
This revised text has been significantly improved by experience we have gained from teaching with the material in various courses and through the sabbatical leave we were granted by Wofford College in 2010-2011. Dr. David Wood, Senior Vice-President and Academic Dean at Wofford has been very understanding of our work and the need for time to do research and writing. He and the college Committee on Non-Curricular Faculty Concerns were most munificent in accommodating this leave. The experiences we gained during the year changed our personal and professional lives immeasurably, and they continue to inspire us in our teaching, research, and writing.
We are unable to stress adequately the value of our time working abroad to the development of this work. For five months we worked with some extremely talented scholars of the Computational Biology Group, the University of Oxford, and we would like to acknowledge the graciousness of Professor David Gavaghan, who agreed to host us. Our focus at Oxford was the modeling of colon cancer, as part of a subgroup concentrating on projects in soft tissue mechanics and cancer. We worked most closely with a then-D. Phil student in mathematics, Ornella Cominetti, who delighted us with her brilliance, her enthusiasm, and her wonderful sense of humor. The time there broadened our experience in modeling and programming (with MATLAB® and Chaste®).
This yearlong adventure was really enabled by a computer scientist we met at a meeting of the International Conference on Computational Science in Krakow, Poland, in 2008. Professor David Abramson, then of Monash University in Melbourne, and more recently of the University of Queensland, Australia, was undoubtedly surprised by our queries about sabbatical positions in Australia and England. Thankfully, he agreed to help us, even providing the essential contact at Oxford. David gave us the opportunity to work within the eResearch and Grid Engineering Laboratory at Monash, where we had five months to do research and write. He encouraged us to present two workshops for graduate students and faculty in computational science at Monash, which provided us with invaluable experiences. Subsequently, one of the participants in the workshop, Dr. Valerie Maxville, who leads the Education Program at iVEC, Western Australia’s supercomputing and eResearch facility, invited us to give a talk and workshop in Perth. Hopefully, our efforts have encouraged more computational applications at Monash and other Australian institutions.
We are indebted to the following reviewers, who offered many valuable constructive criticisms:
Rob Cole, Evergreen State University
Richard Hull, Lenoir-Rhyne College
James Noyes, Wittenberg College
Bob Panoff, The Shodor Foundation
Sylvia Pulliam, Western Kentucky University
Joseph Sloan, Wofford College
Chuck Swanson, University of Minnesota
David Sykes, Wofford College
Peter Turner, Clarkson University
Ignatios Vakalis, Capital University
Second Edition Table of Contents and/or Module Reviewers:
Anne Catllá, Wofford College
Melanie Correll, University of Florida at Gainesville
Stephen Davies, Mary Washington University
Charles Epstein, University of Pennsylvania
David Joiner, Kean University
Hong Liu, Embry-Riddle
Richard Salter, Oberlin College
Joseph Sloan, Wofford College
David Sykes, Wofford College
Carlo Tomasi, Duke University
Vickie Kearn, Senior Editor at Princeton University Press, unfailingly supported us in the preparation of the first edition, which was a novel project in an emerging discipline. She has always had a clear understanding of the project and provided excellent guidance. In the same spirit, Vickie has been enthusiastic in the revision of that project. Her vision and trust have been remarkable, and we reiterate our gratitude for all that she has done to facilitate our latest efforts.
We are so grateful to the extraordinarily capable team at Princeton University Press who helped craft the second edition of this text. Quinn Fusting was always our “go to” person for answers and logistics. Debbie Tegarden very ably guided production, encouraging everyone else in the process. We were delighted to work again with Dimitri Karetnikov, who continues to transform mere figures into art, and Lorraine Doneker, who fashioned another attractive design. We were so fortunate to have Bytheway Publishing Services, directed by Lori Holland, working so carefully and capably again on the typesetting and composition of this very technical and complex project. Thanks also go to Linda Thompson, who skillfully copyedited this edition.
Linda Stoudt, George’s cousin, has been so generous in allowing us to display some of her talent on the covers of both editions of our text. Everything that she does is done with loving care and powerful intellect.
There is no person more responsible for our writing this text than Dr. Robert M. Panoff of the Shodor Education Foundation/National Computational Science Institute. From the first Shodor workshop we attended to the present, Bob has been the source—ideas, encouragement and support. Bob has helped us in countless ways, including traveling to Australia to make the first workshop on computational thinking a resounding success. Moreover, the NSF-funded Blue Waters Undergraduate Petascale Education Program, for which he was a co-PI, funded development of six educational modules, which were preliminary versions of modules in this second edition, and internships for three students, who assisted us with HPC materials. He is passionate about computational science and computational science education, and he is enormously generous with his time and ideas. We are indebted to him for our professional transformation that has facilitated the development of the computational science program at Wofford and the creation of this book.
Our parents Isabell and Carroll Buzzett and Douglas and George Shiflet, Sr., worked so tirelessly to make our lives intense, joyful, and stimulating. We were blessed and inspired by their living efforts, and we miss them. Hopefully, they would be pleased by what we have been doing with our lives.
This book has been a labor of love, which has encouraged us both to grow as teachers and writers. The development of the text has been fun, though complicated; and we have many to thank for their support, collaboration, and patience. First, we must acknowledge our colleagues and students from whom we learn every day. In particular, we want single out one colleague and two very capable students. Professor David Sykes was extremely helpful in his extensive review of the manuscript, providing many useful suggestions. David Harmon was an invaluable aid in preparing the glossary and verifying answers to the exercises and tutorials, and Jonathan DeBusk worked very hard to ensure that the references conformed to the proper style for publication.
We are very appreciative of the sabbaticals that Wofford College gave us and of the consistent support and encouragement by Dr. Dan Maultsby, Senior Vice-President and Academic Dean. The financial support provided by the National Science Foundation for computational science at Wofford ("Enhancing Computation in the Sciences," NSF CCLI Proof-of-Concept Grant No. 0087979) was essential in the development of the program and supporting materials.
We are indebted to the following reviewers, who offered many valuable constructive criticisms:
Rob Cole, Evergreen State University
Richard Hull, Lenoir-Rhyne College
James Noyes, Wittenberg College
Bob Panoff, The Shodor Foundation
Sylvia Pulliam, Western Kentucky University
Joseph Sloan, Wofford College
Chuck Swanson, University of Minnesota
David Sykes, Wofford College
Peter Turner, Clarkson University
Ignatios Vakalis, Capital University
Vickie Kearn, Senior Editor at Princeton, had a clear understanding of the project and provided excellent guidance. We thank you, Vickie, for your vision, trust, and encouragement. Meera Vaidyanathan and Ellen Foos very ably orchestrated production. Dimitri Karetnikov worked his magic on our figures to transform them into art. Thanks also go to Jennifer Slater of Running Dogs Editorial Services for her accurate and insightful copyediting and to Lorraine Doneker for the attractive design.
Dr. Robert M. Panoff of the Shodor Education Foundation has been more than a source of ideas and information for this project. His passion and generosity are remarkable and have been our inspiration. Bob and his very able colleagues at Shodor have and continue to do amazing things for computational science education.
Ultimately we thank our parents, Isabell and Carroll Buzzett and Douglas and George Shiflet, Sr., who throughout their lives have given us boundless love and support. Words are inadequate to express our appreciation. Only Isabell remains, and she continues to delight us each day with her wisdom and wit. Obviously, we are where we are today because they were there for us.
Dedicated to
Robert K. Cralle, Theodore H. Einwohner, and George A. Michael
Lawrence Livermore National Laboratory
and
Robert M. Panoff
The Shodor Education Foundation,
whose friendship and guidance we have treasured
We wish to thank the National Computational Science Institute’s NSF-funded Blue Waters Undergraduate Petascale Education Program and Blue Waters Student Internship Program for providing internships for the following excellent Wofford College students: Shay M. Ellison, Jesse A. Hanley, Whitney Sanders, and Daniel S. Couch. The interns developed high performance computing programs and tutorials to accompany various modules, linked from the main page, by Angela Shiflet and George Shiflet. We deeply appreciate the hard work, enthusiasm, and contributions of these fine collaborators.
A number of talented students have implemented this website. Charles Johnson designed the website for the online modules, determined how to do the Javascript for the Quick Review Questions, and placed the first modules on the web. His design and extensive work have served as models for future online modules. Diana Jackson continued his efforts, adding numerous modules to the website even while studying abroad. Bishop Ravenel implemented the online review form and associated database. Michael Baker, Trey Wall, David Harmon, and Heidi Bostic tested various tutorials and helped to generate the answer files. Daniel Harris did a marvelous job in designing and implementing the website for the textbook and in developing the instructors' password system with database.
Most recently, Wofford graduates Nick Napier and Mayfield Reynolds have modernized the website. Nick developed a new design, which Mayfield expanded. Mayfield’s excellent work included additional features, enhanced security, version control, and migration to a new server.
So many people and organizations have contributed and continue to contribute to development of Wofford College's Emphasis in Computational Science (ECS) and the associate education materials. We are eternally grateful to each of them.
Dr. Dan Maultsby, former Academic Dean, and Wofford College have been very supportive of the program from its inception. Representatives from the sciences met for over a year to discuss requirements for the program. Chairs of Biology, Chemistry, Computer Science, Mathematics, Physics, and Psychology signed the curriculum proposal, and the faculty passed the program unanimously in 1998.
In 2001, the National Science Foundation awarded Wofford College a CCLI Proof-of-Concept Grant (No. 0087979) for the project "Enhancing Computation in the Sciences" to help development of the undergraduate computational science program at Wofford, creation of extensive online computational science educational materials, and promotion of computational science education nationally.
Dr. Dan Welch of Wofford's Physics Department was responsible for purchase of hardware and associated software for the formation of a computational science computer network.
The Data and Visualization course used the late Dr. Steve Cunningham's excellent computer graphics materials with its numerous examples in the sciences. Originally developed with NSF funding, the materials were the basis for his computer graphics textbook, Computer Graphics: Programming, Problem Solving, and Visual Communication (Prentice Hall, 2007). Steve generously advised us on the topics to cover for a half-semester introduction to scientific visualization and provided much encouragement for our program.
Before and during the period of grant funding, Dr. Boyce Lawton wisely assisted in project evaluation.
From existing scientific databases, Dr. Orlando Karam created MySQL databases, which students in Data and Visualization have used extensively.
Dr. Sylvia Pulliam from Western Kentucky University was very supportive in class testing our online modules and in reviewing these materials and a draft of the resulting textbook Introduction to Computational Science: Modeling and Simulation for the Sciences. Dr. Joe Sloan also used and expertly evaluated the online and text modules in courses. Dr. David Sykes proofread and evaluated this material carefully and extensively, providing many valuable suggestions. Dr. Robert Panoff of the Shodor Education Foundation was particularly helpful in reviewing the text and giving insightful suggestions on helping students learn the process of modeling. Dr. Rob Cole from Evergreen State University aptly reviewed physics-related modules, while Dr. Alliston Reid was the inspiration and evaluator for a psychology module. Others, listed in the textbooks' acknowledgements above were also extremely helpful with their suggestions and assistance.