Molecular dynamics simulations 2015

Overview These course notes are compiled, based on previous course materials, for the Moscow Engineering Physics Institute (MePhi) in Dec 2015, but may be used freely by anybody interested. Aim: The aim of the course materials is to provide a practical introduction into modern molecular dynamics simulations methods used in materials physics. Prerequisites: Knowledge of the basics of programming and the Unix environment, the structure of matter and thermodynamics. The course is also suited to chemists. Contents: Visualization and animation of atomic data. Molecular dynamics simulations, which enable following the motion of a set of pointlike objects (typically but not necessarily atoms). During the course, the students get to write in a guided manner their own molecular dynamics code, capable of simulating atom motion in simple metals. Genetic algorithm and conjugate gradient energy minimization of atomic systems. Overview of quantum mechanical and classical models of atomic interaction, and a detailed description of modern classical force models for metals, semiconductors, ionic and organic materials. Responsible persons: Prof. Kai Nordlund and Doc. Flyura Djurabekova Literature: lecture notes. For background material I recommend the books: Allen, Tildesley: "Computer simulation of Liquids" (Oxford University Press, Oxford, England, 1989); still a must-read for a molecular dynamics specialist. D. Frenkel, B. Smit: Understanding Molecular Simulation: From Algorithms to Applications, 2nd edition (Academic Press, 2001) A. R. Leach: Molecular modelling: Principles and applications, 2nd edition (Prentice Hall, 2001) Related materials: Short tutorial notes and animations on molecular dynamics and irradiation effects

Lecture notes