.

0 (hodnocen0 x )

BK

2nd ed.

Cambridge : Cambridge University, 2004

xiii,549 s. : il.

ISBN 0-521-82568-7 (váz.)

Obsahuje grafy, rejstřík

Bibliografie na s. 519-531

Dynamika molekulární - simulace počítačová - příručky

Simulace počítačová - dynamika molekulární - příručky

000005980

Contents // 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 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 82 // v // Contents // vi // 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 // Contents vii // 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 // viii Contents // 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