Gerhard Zumbusch

Particle models play an important role in many applications in physics, chemistry and biology. They can be studied on the computer with the help of molecular dynamics simulations. This book presents in detail both the necessary numerical methods and techniques (linked-cell method, SPME-method, tree codes, multipole technique) and the theoretical background and foundations. It illustrates the aspects modelling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. Furthermore, detailed explanations are given to the different steps of numerical simulation, and code examples are provided. With the description of the algorithms and the presentation of the results of various simulations from the areas material science, nanotechnology, biochemistry and astrophysics, the reader of this book will be able to write his own programs for molecular dynamics step by step and to run successful experiments.

Particle models play an important role in many applications in physics, chemistry and biology. They can be studied on the computer with the help of molecular dynamics simulations. This book presents in detail both the necessary numerical methods and techniques (linked-cell method, SPME-method, tree codes, multipole technique) and the theoretical background and foundations. It illustrates the aspects modelling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. Furthermore, detailed explanations are given to the different steps of numerical simulation, and code examples are provided. With the description of the algorithms and the presentation of the results of various simulations from the areas material science, nanotechnology, biochemistry and astrophysics, the reader of this book will be able to write his own programs for molecular dynamics step by step and to run successful experiments.

Numerical simulation promises new insight in science and engineering. In ad­ dition to the traditional ways to perform research in science, that is laboratory experiments and theoretical work, a third way is being established: numerical simulation. It is based on both mathematical models and experiments con­ ducted on a computer. The discipline of scientific computing combines all aspects of numerical simulation. The typical approach in scientific computing includes modelling, numerics and simulation, see Figure l. Quite a lot of phenomena in science and engineering can be modelled by partial differential equations (PDEs). In order to produce accurate results, complex models and high resolution simulations are needed. While it is easy to increase the precision of a simulation, the computational cost of doing so is often prohibitive. Highly efficient simulation methods are needed to overcome this problem. This includes three building blocks for computational efficiency, discretisation, solver and computer. Adaptive mesh refinement, high order and sparse grid methods lead to discretisations of partial differential equations with a low number of degrees of freedom. Multilevel iterative solvers decrease the amount of work per degree of freedom for the solution of discretised equation systems. Massively parallel computers increase the computational power available for a single simulation.

Das Buch behandelt Methoden des wissenschaftlichen Rechnens in der Moleküldynamik, einem Bereich, der in vielen Anwendungen der Chemie, der Biowissenschaften, der Materialwissenschaften, insbesondere der Nanotechnologie, sowie der Astrophysik eine wichtige Rolle spielt. Es führt in die wichtigsten Simulationstechniken zur numerischen Behandlung der Newtonschen Bewegungsgleichungen ein. Der Schwerpunkt liegt hierbei auf der schnellen Auswertung kurz- und langreichweitiger Kräfte mittels Linked Cell-, P$/\3$M-, Baum- und Multipol-Verfahren, sowie deren paralleler Implementierung und Lastbalancierung auf Rechensystemen mit verteiltem Speicher. Die einzelnen Kapitel beinhalten darüberhinaus detailierte Hinweise, um die Verfahren Schritt für Schritt in ein Programmpaket umzusetzen. In zahlreichen farbigen Abbildungen werden Simulationsergebnisse für eine Reihe von Anwendungen präsentiert.