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The Art of Molecular Dynamics Simulation, Second Edition

Book Description

The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

Table of Contents

  1. Cover
  2. Half Title
  3. Title Page
  4. Copyright
  5. Contents
  6. Preface to the first edition
  7. Preface to the second edition
  8. About the software
  9. 1. Introduction
    1. 1.1 Historical background
    2. 1.2 Computer simulation
    3. 1.3 Molecular dynamics
    4. 1.4 Organization
    5. 1.5 Further reading
  10. 2. Basic molecular dynamics
    1. 2.1 Introduction
    2. 2.2 Soft-disk fluid
    3. 2.3 Methodology
    4. 2.4 Programming
    5. 2.5 Results
    6. 2.6 Further study
  11. 3. Simulating simple systems
    1. 3.1 Introduction
    2. 3.2 Equations of motion
    3. 3.3 Potential functions
    4. 3.4 Interaction computations
    5. 3.5 Integration methods
    6. 3.6 Initial state
    7. 3.7 Performance measurements
    8. 3.8 Trajectory sensitivity
    9. 3.9 Further study
  12. 4. Equilibrium properties of simple fluids
    1. 4.1 Introduction
    2. 4.2 Thermodynamic measurements
    3. 4.3 Structure
    4. 4.4 Packing studies
    5. 4.5 Cluster analysis
    6. 4.6 Further study
  13. 5. Dynamical properties of simple fluids
    1. 5.1 Introduction
    2. 5.2 Transport coefficients
    3. 5.3 Measuring transport coefficients
    4. 5.4 Space–time correlation functions
    5. 5.5 Measurements
    6. 5.6 Further study
  14. 6. Alternative ensembles
    1. 6.1 Introduction
    2. 6.2 Feedback methods
    3. 6.3 Constraint methods
    4. 6.4 Further study
  15. 7. Nonequilibrium dynamics
    1. 7.1 Introduction
    2. 7.2 Homogeneous and inhomogeneous systems
    3. 7.3 Direct measurement
    4. 7.4 Modified dynamics
    5. 7.5 Further study
  16. 8. Rigid molecules
    1. 8.1 Introduction
    2. 8.2 Dynamics
    3. 8.3 Molecular construction
    4. 8.4 Measurements
    5. 8.5 Rotation matrix representation
    6. 8.6 Further study
  17. 9. Flexible molecules
    1. 9.1 Introduction
    2. 9.2 Description of molecule
    3. 9.3 Implementation details
    4. 9.4 Properties
    5. 9.5 Modeling structure formation
    6. 9.6 Surfactant models
    7. 9.7 Surfactant behavior
    8. 9.8 Further study
  18. 10. Geometrically constrained molecules
    1. 10.1 Introduction
    2. 10.2 Geometric constraints
    3. 10.3 Solving the constraint problem
    4. 10.4 Internal forces
    5. 10.5 Implementation details
    6. 10.6 Measurements
    7. 10.7 Further study
  19. 11. Internal coordinates
    1. 11.1 Introduction
    2. 11.2 Chain coordinates
    3. 11.3 Kinematic and dynamic relations
    4. 11.4 Recursive description of dynamics
    5. 11.5 Solving the recursion equations
    6. 11.6 Implementation details
    7. 11.7 Measurements
    8. 11.8 Further study
  20. 12. Many-body interactions
    1. 12.1 Introduction
    2. 12.2 Three-body forces
    3. 12.3 Embedded-atom approach
    4. 12.4 Further study
  21. 13. Long-range interactions
    1. 13.1 Introduction
    2. 13.2 Ewald method
    3. 13.3 Tree-code approach
    4. 13.4 Fast-multipole method
    5. 13.5 Implementing the fast-multipole method
    6. 13.6 Results
    7. 13.7 Further study
  22. 14. Step potentials
    1. 14.1 Introduction
    2. 14.2 Computational approach
    3. 14.3 Event management
    4. 14.4 Properties
    5. 14.5 Generalizations
    6. 14.6 Further study
  23. 15. Time-dependent phenomena
    1. 15.1 Introduction
    2. 15.2 Open systems
    3. 15.3 Thermal convection
    4. 15.4 Obstructed flow
    5. 15.5 Further study
  24. 16. Granular dynamics
    1. 16.1 Introduction
    2. 16.2 Granular models
    3. 16.3 Vibrating granular layer
    4. 16.4 Wave patterns
    5. 16.5 Further study
  25. 17. Algorithms for supercomputers
    1. 17.1 Introduction
    2. 17.2 The quest for performance
    3. 17.3 Techniques for parallel processing
    4. 17.4 Distributed computation
    5. 17.5 Shared-memory parallelism
    6. 17.6 Techniques for vector processing
    7. 17.7 Further study
  26. 18. More about software
    1. 18.1 Introduction
    2. 18.2 Structures and macro definitions
    3. 18.3 Allocating arrays
    4. 18.4 Utility functions
    5. 18.5 Organizing input data
    6. 18.6 Configuration snapshot files
    7. 18.7 Managing extensive computations
    8. 18.8 Header files
  27. 19. The future
    1. 19.1 Role of simulation
    2. 19.2 Limits of growth
    3. 19.3 Visualization and interactivity
    4. 19.4 Coda
  28. Appendix
  29. References
  30. Function index
  31. Index
  32. Colophon