### Chapter 10 - Simulation Schemes, Softwares, Lab Practice and Applications

The focus of this chapter is to study methods, skills and applications of atomistic simulation. Accompanying to this Chapter a Computational Simulation Laboratory Infrastructure (CSLI) is constructed which can be downloaded* and used for lab practice. CSLI contains 12 UNITS which is with one-to-one correspondence to the 12 Sections of this Chapter. They are separated into three parts:

- Part 1 (Section 10.0 to 10.5): This part introduces basics of computational simulations. It starts with an introduction of the UNIX system, analyses of a simple MD code, and basic knowledge of FORTRAN90 computer language. It introduces GULP software which can be used for optimization of atomistic static lattices, calculation for defects and determination of potential parameters. It also introduces the visualization tools and public MD software DL_POLY.
- Part 2 (Section 10.6-10.8): Simulation applications in metals and ceramics by MD.
- Part 3 (Section 10.9-10.12): The NAMD software is introduced that can be used for simulation of protein-water system. A brief introduction of LAMMPS is also given.

Each UNIT in CSLI contains files for computer simulation and the corresponding section describes the simulation processes operated in that UNIT. This chapter is written with a style which can be used both for laboratory class of computational simulation and self-learning text of readers at different levels.

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