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Lectures in Molecular Simulation

Clicking on any of the buttons below will launch a self-paced lecture presentation on the indicated topic. Each topic comprises approximately two hours of lecture material. The modules assume prior knowledge of statistical mechanics at an undergraduate level and programming ability in C.

The modules are largely self-contained except that some material common to both Monte Carlo and molecular dynamics, such as the calculation of pair interactions and periodic boundary conditions, is described in greater detail in the Monte Carlo sections. Taken together, modules 1-6 and 7-12 represent introductory courses in Monte Carlo and molecular dynamics, respectively.

1.
Introduction to Monte Carlo
7.
Introduction to Molecular Dynamics

2.
Monte Carlo Simulation I
8.
Initialisation and MD Basics

3.
Monte Carlo Simulation II
9.
Forces, Constraints and MD Ensembles

4.
Ensembles and Monte Carlo Simulation
10
Quantities in Molecular Dynamics

5.
Intermolecular Potentials
11.
Introduction to Molecules

6.
Algorithms for Phase Coexistence
12.
Introduction to NEMD

http://www.mdbbs.org/thread-6672-1-1.html
http://www.swinburne.edu.au/ict/research/cms/online_courses.htm

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Software and Data
Please click the appropriate link to download CMS authored software (zip files).
Software from R.J. Sadus, "Molecular Simulation of Fluids: Theory, Algorithms and Object-Orientation," Elsevier, Amsterdam 1999 (reprinted in paperback in 2002).

Monte Carlo programs in C++ Molecular dynamics programs in C++
Combined Monte Carlo/molecular dynamics programs in C++

Confguration file data used in figure 4 of G.-W. Wu and R.J. Sadus, "New phase for one-component hard spheres." J. Chem. Phys. 120, 11686-11691 (2004).

Fig. 4a Metastable fluid (phenomenon I) Fig. 4b New Phase (phenomenon III)
Fig. 4c Solid (phenomenon II)
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Dissertations of the Centre for Molecular Simulation
Recent PhD DissertationsPlease click the links below to obtain a PDF copy of each chapter.
Hunt, T.A., "Theory and Simulation of Polymer Liquids under Extensional and Shear Flows ", Swinburne University of Technology (2008).

Abstract and Contents Chapter 1: Introduction Chapter 2: Models and Theory of Polymer Rheology Chapter 3: Molecular Simulation Chapter 4: Comparison of FENE and FJC Molecules Chapter 5: Diffusion in Shear and Extensional Flows Chapter 6: Conclusion Appendix 1
References

Frascoli, F., "Chaotic and Rheological Properties of Liquids Under Planar Shear and Elongational
Flows", Swinburne University of Technology (2007).

Abstract and Contents Chapter 1: Introduction to Nonequilibrium Molecular Dynamics Chapter 2: Molecular Dynamics Simulation of Planar Elongational Flow at Constant Pressure and Temperature Chapter 3: Chaos in Nonequilibrium Liquid Systems Chapter 4: Chaotic Properties of Liquids Under Planar Shear and Elongational Flows Chapter 5: Conclusions and Recommendations Appendix 1 Appendix 2
References

Bosko, J.T., "Molecular Simulation of Dendrimers Under Shear," Swinburne University of Technology (Date of graduation: November, 2005).

Abstract and Contents Chapter 1: Introduction Chapter 2: Dendrimers Chapter 3: Reheology of Molecular Fluids Chapter 4: Molecular Simulation Chapter 5: Flow Properties of Dendrimers Under Shear Chapter 6: Microscopic Properties of Dendrimers Chapter 7: Conclusions and Recommendations
References

Zhang, J., "Computer Simulation of Nanorheology for Inhomogeneous Fluids," Swinburne University of Technology (Date of graduation: November, 2005).

Abstract and Contents Chapter 1: General Introduction Chapter 2: Hydrodynamic Theory Chapter 3: Simulation Methodology Chapter 4: Parallel Programing with MPI Chapter 5: Simulation of Atomic Poiseulle Flow under the Influence of Three-Body Forces Chapter 6: Non-Local linear Hydrodynamic Constitutive Model Chapter 7: Simulation of Confined Polymeric Fluids Undergoing Poiseulle Flow Chapter 8: Summary and Conclusions
References

Ge, J., "The State Point Dependence of Classical Fluids under Shear," Swinburne University of Technology (Date of graduation: March, 2004).

Abstract and Contents Chapter 1: Introduction Chapter 2: Literature Review Chapter 3: Shear Flow Chapter 4: Molecular Simulation Chapter 5: State Point Dependence of Power Exponents Chapter 6: Use of Equilibrium and Nonequilibrium Molecular Dynamics to Determine Solid-Liquid Coexistence at Equilibrium Chapter 7: Barker-Fisher-Watts Fluid: Its Power Exponents and Liquid-Solid Boundary Chapter 8: Use of TTCF to Calculate the Viscosity in a Weak Field Chapter 9: Conclusions
References

Wang, J.-L., "Global Phase Diagrams and Critical Phenomena of Binary Mixtures," Swinburne University of Technology (Date of graduation: October 15, 2003).

Abstract and Contents Chapter 1: Introduction Chapter 2: Critical Phenomena and Fluid Theories Chapter 3: Equations of State Chapter 4: Global Phase Diagrams Chapter 5: Global Phase Diagram for Binary Mixtures of "Hard Sphere + van der Waals" molecules: calculations with the Guggenheim Equation of State Chapter 6: Global Phase Diagrams in terms of Pure Component Properties
Chapter 7: Conclusions and Recommendations

Marcelli, G., "The Role of Three-Body Interactions on the Equilibrium and Non-Equilibrium Properties of Fluids from Molecular Simulation," Swinburne University of Technology (Date of graduation: October 11, 2001).

Abstract and Contents Chapter 1: Molecular Simulation of Fluids Chapter 2: Theory and Computation Techniques Chapter 3: Investigation of Three-Body Interactions on the Phase Behaviour of Noble Gases Chapter 4: Shear Rate Dependence of Pressure, Energy and Viscosity in Planar Couette Flow Chapter 5: Conclusions and Recommendations Appendix 1: Long-Range Correction for BFW Potential Appendix 2: Three-Body Potential Molecular Simulation Implementation
References

Wei, Y.S., "Prediction of the Fluid Phase Equilibria of Binary and Ternary Mixtures," Swinburne University of Technology (Date of graduation: May 1999).

Abstract and Contents Chapter 1: Introduction Chapter 2: Theory of Fluids Chapter 3: Equations of State Chapter 4: Criteria for Equilibria and Calculation Techniques Chapter 5: Fluid Phase Equilibria of Binary Mixtures Chapter 6: Fluid Phase Equilibria of Ternary Mixtures
Chapter 7: Conclusions