| Computer Simulation - a Key Technology | p. 1 |
| From the Schrodinger Equation to Molecular Dynamics | p. 17 |
| The Schrodinger Equation | p. 17 |
| A Derivation of Classical Molecular Dynamics | p. 21 |
| TDSCF Approach and Ehrenfest Molecular Dynamics | p. 21 |
| Expansion in the Adiabatic Basis | p. 24 |
| Restriction to the Ground State | p. 26 |
| Approximation of the Potential Energy Hypersurface | p. 26 |
| An Outlook on Methods of Ab Initio Molecular Dynamics | p. 30 |
| The Linked Cell Method for Short-Range Potentials | p. 37 |
| Time Discretization - the Stormer-Verlet Method | p. 40 |
| Implementation of the Basic Algorithm | p. 46 |
| The Cutoff Radius | p. 53 |
| The Linked Cell Method | p. 56 |
| Implementation of the Linked Cell Method | p. 58 |
| First Application Examples and Extensions | p. 64 |
| Collision of Two Bodies I | p. 66 |
| Collision of Two Bodies II | p. 68 |
| Density Gradient | p. 72 |
| Rayleigh-Taylor Instability | p. 73 |
| Rayleigh-Benard Convection | p. 79 |
| Surface Waves in Granular Materials | p. 82 |
| Thermostats, Ensembles, and Applications | p. 86 |
| Thermostats and Equilibration | p. 87 |
| Statistical Mechanics and Thermodynamic Quantities | p. 93 |
| Phase Transition of Argon in the NVT Ensemble | p. 96 |
| The Parrinello-Rahman Method | p. 104 |
| Phase Transition of Argon in the NPT Ensemble | p. 107 |
| Parallelization | p. 113 |
| Parallel Computers and Parallelization Strategies | p. 113 |
| Domain Decomposition for the Linked Cell Method | p. 122 |
| Implementation | p. 128 |
| Performance Measurements and Benchmarks | p. 139 |
| Application Examples | p. 146 |
| Collision of Two Bodies | p. 146 |
| Rayleigh-Taylor Instability | p. 148 |
| Extensions to More Complex Potentials and Molecules | p. 151 |
| Many-Body Potentials | p. 151 |
| Cracks in Metals - Finnis-Sinclair Potential | p. 152 |
| Phase Transition in Metals - EAM Potential | p. 160 |
| Fullerenes and Nanotubes - Brenner Potential | p. 167 |
| Potentials with Fixed Bond Structures | p. 181 |
| Membranes and Minimal Surfaces | p. 181 |
| Systems of Linear Molecules | p. 186 |
| Outlook to More Complex Molecules | p. 202 |
| Time Integration Methods | p. 211 |
| Errors of the Time Integration | p. 212 |
| Symplectic Methods | p. 221 |
| Multiple Time Step Methods - the Impulse Method | p. 226 |
| Constraints - the RATTLE Algorithm | p. 230 |
| Mesh-Based Methods for Long-Range Potentials | p. 239 |
| Solution of the Potential Equation | p. 243 |
| Boundary Conditions | p. 243 |
| Potential Equation and Potential Decomposition | p. 244 |
| Decomposition of the Potential Energy and of the Forces | p. 248 |
| Short-Range and Long-Range Energy and Force Terms | p. 250 |
| Short-Range Terms - Linked Cell Method | p. 250 |
| Long-Range Terms - Fast Poisson Solvers | p. 252 |
| Some Variants | p. 258 |
| Smooth Particle-Mesh Ewald Method (SPME) | p. 260 |
| Short-Range Terms | p. 261 |
| Long-Range Terms | p. 263 |
| Implementation of the SPME method | p. 273 |
| Application Examples and Extensions | p. 281 |
| Rayleigh-Taylor Instability with Coulomb Potential | p. 281 |
| Phase Transition in Ionic Microcrystals | p. 284 |
| Water as a Molecular System | p. 287 |
| Parallelization | p. 294 |
| Parallelization of the SPME Method | p. 294 |
| Implementation | p. 299 |
| Performance Measurements and Benchmarks | p. 302 |
| Example Application: Structure of the Universe | p. 306 |
| Tree Algorithms for Long-Range Potentials | p. 313 |
| Series Expansion of the Potential | p. 314 |
| Tree Structures for the Decomposition of the Far Field | p. 320 |
| Particle-Cluster Interactions and the Barnes-Hut Method | p. 325 |
| Method | p. 326 |
| Implementation | p. 328 |
| Applications from Astrophysics | p. 339 |
| Parallel Tree Methods | p. 341 |
| An Implementation with Keys | p. 343 |
| Dynamical Load Balancing | p. 357 |
| Data Distribution with Space-Filling Curves | p. 359 |
| Applications | p. 366 |
| Methods of Higher Order | p. 370 |
| Implementation | p. 371 |
| Parallelization | p. 376 |
| Cluster-Cluster Interactions and the Fast Multipole Method | p. 377 |
| Method | p. 377 |
| Implementation | p. 382 |
| Error Estimate | p. 385 |
| Parallelization | p. 386 |
| Comparisons and Outlook | p. 387 |
| Applications from Biochemistry and Biophysics | p. 391 |
| Bovine Pancreatic Trypsin Inhibitor | p. 392 |
| Membranes | p. 394 |
| Peptides and Proteins | p. 398 |
| Protein-Ligand Complex and Bonding | p. 408 |
| Prospects | p. 413 |
| Appendix | p. 417 |
| Newton's, Hamilton's, and Euler-Lagrange's Equations | p. 417 |
| Suggestions for Coding and Visualization | p. 418 |
| Parallelization by MPI | p. 421 |
| Maxwell-Boltzmann Distribution | p. 425 |
| Parameters | p. 428 |
| References | p. 431 |
| Index | p. 467 |
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