Table of contents for The art of molecular dynamics simulation / D.C. Rapaport.


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Preface to the first edition                             page ix
Preface to the second edition                                xii
About the software                                           xiii
1    Introduction                                                   1
1.1   Historical background                                  1
1.2   Computer simulation                                    2
1.3   Molecular dynamics                                     4
1.4   Organization                                           8
1.5   Further reading                                       10
2    Basic molecular dynamics                                      11
2.1  Introduction                                           11
2.2   Soft-disk fluid                                       11
2.3   Methodology                                           18
2.4   Programming                                           20
2.5   Rcsults                                               34
2.6   Further study                                         43
3    Simulating simple systems                                    44
3.1  Introduction                                           44
3.2   Equations of motion                                   44
3.3   Potential functions                                   46
3.4  Interaction computations                               49
3.5  Integration methods                                    60
3.6  Initial state                                          67
3.7   Performance measurements                              74
3.8   Trajectory sensitivity                                77
3.9   Further study                                         82



4    Equilibrium properties of simple fluids                      83
4.1   Introduction                                          83
4.2   Thermodynamic measurements                            84
4.3   Structure                                             90
4.4   Packing studies                                       96
4.5   Cluster analysis                                     112
4.6   Further study                                        118
5    Dynamical properties of simple fluids                       120
5.1  Introduction                                          120
5.2   Transport coefficients                               120
5.3   Measuring transport coefficients                     124
5.4   Space-time correlation functions                     134
5.5   Measurements                                         145
5.6   Further study                                        152
6    Alternative ensembles                                       153
6.1  Introduction                                          153
6.2   Feedback methods                                     154
6.3   Constraint methods                                   165
6.4   Further study                                        174
7    Nonequilibrium dynamics                                     176
7.1   Introduction                                         176
7.2   Homogeneous and inhomogeneous systems                176
7.3   Direct measurement                                   177
7.4   Modified dynamics                                    188
7.5   Further study                                        198
8    Rigid molecules                                             199
8.1  Introduction                                          199
8.2   Dynamics                                             200
8.3   Molecular construction                               216
8.4   Measurements                                         222
8.5   Rotation matrix representation                       232
8.6   Further study                                        243
9    Flexible molecules                                          245
9.1  Introduction                                          245
9.2   Description of molecule                              245
9.3   Implementation details                               247
9.4   Properties                                           251
9.5   Modeling structure formation                         256



9.6   Surfactant models                                   257
9.7   Surfactant behavior                                 262
9.8   Further study                                       266
10   Geometrically constrained molecules                        267
10.1 Introduction                                         267
10.2  Geometric constraints                               267
10.3  Solving the constraint problem                      270
10.4 Internal forces                                      278
10.5 Implementation details                               286
10.6  Measurements                                        291
10.7  Further study                                       294
11   Internal coordinates                                       296
11.1 Introduction                                         296
11.2  Chain coordinates                                   296
11.3  Kinematic and dynamic relations                     298
11.4  Recursive description of dynamics                   299
11.5  Solving the recursion equations                     308
11.6 Implementation details                               317
11.7  Measurements                                        322
11.8  Further study                                       325
12   Many-body interactions                                     326
12.1 Introduction                                         326
12.2  Three-body forces                                   326
12.3  Embedded-atom approach                              332
12.4  Further study                                       343
13   Long-range interactions                                    344
13.1 Introduction                                         344
13.2  Ewald method                                        345
13.3  Tree-code approach                                  359
13.4  Fast-multipole method                               365
13.5 Implementing the fast-multipole method               373
13.6  Results                                             386
13.7  Further study                                       389
14   Step potentials                                            391
14.1 Introduction                                         391
14.2  Computational approach                              392
14.3  Event management                                   403
14.4  Properties                                         411
14.5  Generalizations                                    414



14.6  Further study                                      417
15   Time-dependent phenomena                                   418
15.1 Introduction                                         418
15.2  Open systems                                        418
15.3  Thermal convection                                  420
15.4  Obstructed flow                                     420
15.5  Further study                                       435
16   Granular dynamics                                          435
16.1 Introduction                                         436
16.2  Granular models                                     436
16.3  Vibrating granular layer                            436
16.4  Wave patterns                                       439
16.5  Further study                                       445
17   Algorithms for supercomputers                              445
17.1 Introduction                                         446
446
17.2  The quest for performance                           446
17.3  Techniques for parallel processing                 447
17.4  Distributed computation                            450
17.5  Shared-memory parallelism                           467
17.6  Techniques for vector processing                    473
17.7  Further study                                       480
18   More about software                                        481
18.1 Introduction                                         481
18.2  Structures and macro definitions                    481
18.3  Allocating arrays                                   487
18.4  Utility functions                                   488
18.5  Organizing input data                               495
18.6  Configuration snapshot files                        498
18.7  Managing extensive computations                     500
18.8  Header files                                        504
19   The future                                                 504
19.1  Role of simulation                                  505
19.2  Limits of growth                                    506
19.3  Visualization and interactivity                     507
19.4  Coda                                                508
Appendix                                                   509
References                                                 519
Function index                                             532
Index                                                      535
Colophon                                                   549
549





Library of Congress Subject Headings for this publication: Condensed matter Computer simulation, Molecular dynamics Computer simulation