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THE ART OF MOLECULAR DYNAMICS SIMULATION
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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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2楼2008-04-19 10:39:31
