Design and Implementation of a General Molecular Dynamics Package

There are numerous codes available for making molecular dynamic simulation. The majority of these are centered on high performance mainly. We’ve moved that focus towards modularity, flexibility and ease of use. Our objective is to design an application which is user friendly, can handle many different kind of simulations and is also easily extendable to fulfill new requirements. In the report we supply you with the theory which is required to understand the principles of a molecular dynamics simulation. The 4 different potentials we’ve used in the software are presented. Additionally we give a comprehensive description of the design and the various design choices we’ve made while making the software. We present a few examples of how the software may be employed and discuss some facets of the performance of the implementation. Ultimately we give our thoughts on the future of the software…


1 Introduction
1.1 Background
1.2 Goal
1.3 Thesis Outline
1.4 Intended Audience
1.5 Summary
2 Molecular Dynamics
2.1 Theory
2.2 A simple MD program
2.3 Potential
2.3.1 Lennard-Jones
2.3.2 Embedded-Atom Method (EAM)
2.3.3 Stillinger-Weber
2.3.4 Terso
2.4 Integration
2.4.1 Verlet
2.4.2 Velocity Verlet
2.4.3 Higher order algorithms
2.5 Possibilities
2.6 Summary
3 MD Sinecura
3.1 Design
3.2 Neighbours
3.2.1 Internal design
3.2.2 External design
3.3 Atom types
3.4 Integration
3.4.1 Internal design
3.4.2 External design
3.5 Thermostat
3.5.1 Velocity Scaling
3.5.2 Andersen Thermostat
3.6 Boundary conditions
3.7 Potential
3.7.1 Framework
3.8 Tabulation
3.9 Sample
3.9.1 Framework
3.10 Initialization of the geometry
3.10.1 Ad hoc method for making advanced surfaces
3.11 Summary
4 Simulation Example
4.1 Initiation
4.1.1 Simulation parameters
4.1.2 Potential parameters
4.1.3 Geometry
4.2 Simulation
4.3 Results
4.4 Summary
5 Performance
5.1 Benchmark
5.1.1 Time per atom and time step
5.2 Cutoff length
5.2.1 Three-body Potentials
5.3 Tabulation
5.4 Numerical vs. Analytical Derivatives
5.5 Data generation
5.6 Summary
6 Discussion
6.1 Future…

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