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li_xinjiang

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[资源] THE ART OF MOLECULAR DYNAMICS SIMULATION

THE ART OF MOLECULAR DYNAMICS SIMULATION
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 Results 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
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 429
15.5 Further study 435
16 Granular dynamics 436
16.1 Introduction 436
16.2 Granular models 436
16.3 Vibrating granular layer 439
16.4 Wave patterns 443
16.5 Further study 445
17 Algorithms for supercomputers 446
17.1 Introduction 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 505
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

[ Last edited by li_xinjiang on 2008-4-19 at 10:41 ]

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