University of Tennessee
Department of Materials Science & Engineering

MSE 614 Course Website

Modeling & Simulation in Materials Science & Engineering: Classical Mechanics
Department of Materials Science & Engineering
University of Tennessee at Knoxville
Notes
  • Four Scales of Modeling


  • Practical User's Guide for ISAAC


  • A Working Person's Guide to Molecular Dynamics


  • A Practical Demonstration of Running a First LAMMPS Simulation on ISAAC


  • Error Analysis (Block Averaging)


  • Interdisciplinary Graduate Minor in Computational Science


  • Visualization


  • Simulation of Metals Using the Embedded Atom Method (EAM) Potential


  • Simulation of Molecules (Intramolecular Degrees of Freedom)


  • Multi-Step Time Integrators: r-ReSPA


  • Thermostats & Barostats
    • Keffer, D.J., Baig, C., Adhangale, P., Edwards, B.J., "A Generalized Hamiltonian-Based Algorithm for Rigorous Equilibrium Molecular Dynamics Simulation in the Canonical Ensemble", J. Non-Newtonian Fluid Mech. 152(1-3) 2008 pp. 129-139. http://dx.doi.org/10.1016/j.jnnfm.2007.10.004
    • Keffer, D.J., Baig, C., Adhangale, P., Edwards, B.J., "A Generalized Hamiltonian-Based Algorithm for Rigorous Equilibrium Molecular Dynamics Simulation in the Isobaric-Isothermal Ensemble", Mol. Sim. 32(5) 2006 p. 345-356. http://dx.doi.org/10.1080/08927020600684345
    • Example Files


  • Rigid Dynamics
    • Notes
    • Example Files
    • Equations of Motion for Rigid Bodies:
      T. F. Miller, M. Eleftheriou, P. Pattnaik, A. Ndirango, D. Newns, and G. J. Martyna, “Symplectic quaternion scheme for biophysical molecular dynamics”, J. Chem. Phys. 116, 2002, p. 8649, doi: 10.1063/1.1473654.


  • Thermodynamic Properties
    • Notes
    • Wang, Q., Keffer, D.J., Petrovan, S., Thomas, J.B., “Molecular Dynamics Simulation of Polyethylene Terephthalate Oligomers”, J. Phys. Chem. B. 114(2), 2010, pp. 786-795, doi: 10.1021/jp909762j.
    • McNutt, N.W., Wang, Q., Keffer, D.J., Rios, O., “Entropy-driven Structure and Dynamics in Carbon Nanocrystallites”, J. Nanoparticle Res. 16 (4), 2014, article # 2365, doi: 10.1007/s11051-014-2365-7.


  • Diffusion
    • Notes
    • Example Files
    • A Practical Introduction to Self-Diffusion Coefficients
    • Frame of Reference for Diffusion:
      Keffer, D.J., Gao, C.Y., Edwards, B.J., “On the Relationship between Fickian Diffusivities at the Continuum and Molecular Levels”, J. Phys. Chem B. 109 2005 pp. 5279-5288, doi: 10.1021/jp0446635.
    • Checking the MSD vs Time Exponent:
      Wang, Q., Keffer, D.J., Petrovan, S., Thomas, J.B., “Molecular Dynamics Simulation of Polyethylene Terephthalate Oligomers”, J. Phys. Chem. B. 114(2), 2010, pp. 786-795, doi: 10.1021/jp909762j.
    • Temperature Dependence of Diffusion Coefficients
      & Examination of RMS Displacements:
      Xiong, R., Odbadrakh, K., Michalkova, A., Luna, J.P., Petrova, T., Keffer, D.J., Nicholson, D.M., Fuentes-Cabrera, M.A., Lewis, J.P., Leszczynski, J., “Evaluation of Functionalized Isoreticular Metal Organic Frameworks (IRMOFs) as Smart Nanoporous Preconcentrators of RDX”, Sensor Actuat B-Chem 148 2010 pp. 459-468, doi: 10.1016/j.snb.2010.05.064.
    • Composition Dependence of Diffusion Coefficients:
      Keffer, D.J., Adhangale, P., “The composition dependence of self and transport diffusivities from molecular dynamics simulations”, Chem. Eng. J. 100 (1-3) 2004 pp. 51-69, doi: 10.1016/j.cej.2003.11.028.
    • Statistical Reliability of Diffusion Coefficients:
      Keffer, D.J., Edwards, B.J., Adhangale, P., “Determination of statistically reliable transport diffusivities from molecular dynamics simulation”, J. Non-Newtonian Fluid Mech. 120 (1-3) 2004 pp. 41-53, doi: 10.1016/j.jnnfm.2004.01.014.
    • Single File Motion:
      Keffer, H.T., McCormick, A.V., D., Davis, “Unidirectional and single-file diffusion in AlPO4-5: molecular dynamics investigations”, Mol. Phys. 87(2) 1996 pp. 367-387, doi: 10.1080/00268979600100241.
    • Sub-Diffusive Motion in an Intermediate Time Scale:
      Calvo-Muñoz, E.M., Esai Selvan, M., Xiong, R., Ojha, M., Keffer, D.J., Nicholson, D.M., Egami, T., “Applications of a General Random Walk Theory for Confined Diffusion”, Phys. Rev. E 83(1) 2011 article # 011120, doi: 10.1103/PhysRevE.83.011120.
    • Non-Equilibrium Measurements of Diffusivity:
      Grant S. Heffelfinger and Frank van Swol, “Diffusion in Lennard-Jones fluids using dual control volume grand canonical molecular dynamics simulation (DCV-GCMD)”, J. Chem. Phys. 100(10) 1994 p. 7548-7552, doi: 10.1063/1.466849.


  • Viscosity
    • Notes
    • (links to references moved inside notes)


  • Thermal Conductivity


  • Structural Properties


  • Two Phase Simulations


  • Restarting Simulations
    • notes forthcoming


  • Evaluating the Coulombic Potential
    • notes forthcoming


  • Reactive Molecular Dynamics
    • Notes
    • guest lecture by Nick McNutt


  • Evaluating the Chemical Potential
    • Notes (forthcoming)
    • guest lecture by Marshall McDonnell


    •

 

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