Sandia National Laboratories
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Contact
Dr. Aidan P. Thompson,
Principal Member of Technical Staff
Scalable Algorithms Department, 1426
Sandia National Laboratories
PO Box 5800, Mail Stop 1322
Albuquerque, New Mexico 87185-1322
USA
Tel: +1 505 844 9702
Fax: +1 505 845 7442
E-mail: athompsATsandiaDOTgov
http://www.cs.sandia.gov/~athomps


Related Links

LAMMPS

SPPARKS

Aidan Thompson
My work deals with the development and application of algorithms for large-scale atomistic simulation of materials on advanced computing platforms. This mostly means adding to and improving the methods available in the LAMMPS molecular dynamics (MD) package. The two biggest limitations of MD are the accuracy of interatomic potentials and accessible timescales, and so these are the things I am most interested in. I also sometimes work on a much faster method called KMC, and have helped develop a parallel KMC code called SPPARKS

Publications

    2013



  1. T.-R. Shan, R. R. Wixom, A. E. Mattsson, and A. P. Thompson , "Atomistic Simulation of Orientation Dependence in Shock-Induced Initiation of Pentaerythritol Tetranitrate," J. Phys. Chem. B, 117 928 (2013).

    2012



  2. S. J. Plimpton and A. P. Thompson , "Computational aspects of many-body potentials," Mat. Res. Soc. Bulletin, 37 513 (2012).

  3. P. L. Theofanis, A. Jaramillo-Botero, W. A. Goddard III, T. R. Mattsson, and A. P. Thompson , "Electron dynamics of shocked polyethylene crystal," Phys. Rev. B, 85 094109 (2012).

  4. J. M. D. Lane, G. S. Grest, A. P. Thompson, K. R. Cochrane, M. Desjarlais, and T. R. Mattsson, "Shock compression of dense polymer and foam systems using molecular dynamics and DFT," Shocked Compression of Condensed Matter, AIP Conf. Proc. 1426 1435 (2012).

  5. A. P. Thompson, J. M. D. Lane, and M. Desjarlais, "Molecular Dynamics Simulation of Dynamic Response of Beryllium," Shocked Compression of Condensed Matter, AIP Conf. Proc. 1426 1311 (2012).

    2011



  6. S. Jayaraman, A. P. Thompson, and O. A. von Lilienfeld, "Molten salt eutectics from atomistic simulations," Phys. Rev. E, 84 030201 (2011).

    2010



  7. H. Asegun, G. Chen, S. J. Plimpton, and A. P. Thompson, "1D-to-3D transition of phonon heat conduction in polyethylene using molecular dynamics simulations," Phys. Rev. B, 82 144308 (2010).

  8. S. V. Zybin, W. A. Goddard, P. Xu, A. C. T. van Duin, and A. P. Thompson, "Physical mechanism of anisotropic sensitivity in pentaerythritol tetranitrate from compressive-shear reaction dynamics simulations," Appl. Phys. Lett., 96 081918 (2010).

  9. S. Martin, A. P. Thompson, E. A. Coutsias and J. P. Watson, "Topology of cyclo-octane energy landscape ," J. Chem. Phys., 132 234115 (2010).

  10. W. M. Brown, A. P. Thompson, and P. A. Schultz, "Efficient Hybrid Evolutionary Optimization of Interatomic Potential Models," J. Chem. Phys., 132 024108 (2010).

  11. T. R. Mattsson, J. M. D. Lane, K. R. Cochrane, M. P. Desjarlais, A. P. Thompson, F. Pierce, and G. S. Grest, "First-Principles and Classical Molecular Dynamics Simulation of Shocked Polymers ," Phys. Rev. B, 81 054103 (2010).

  12. S. Jayaraman, A. P. Thompson, O. A. von Lilienfeld and E. J. Maginn, "Molecular simulation of the thermal and transport properties of three alkali nitrate salts," Ind. & Eng. Chem. Res., 49 559 (2010).

    2009



  13. A. P. Thompson, S. J. Plimpton, and W. Mattson, "General Formulation of Pressure and Stress Tensor for Arbitrary Many-body Interaction Potentials under Periodic Boundary Conditions," J. Chem. Phys., 131 154107 (2009).

  14. J. Budzien, A. P. Thompson, and S. V. Zybin, "Reactive Molecular Dynamics Simulations of Shock Through a Single Crystal of Pentaerythritol Tetranitrate," J. Phys. Chem. B, 113 13142 (2009).

  15. A. P. Thompson, J. M. D. Lane , M. P. Desjarlais and M. I. Baskes, "Molecular Dynamics Simulation of Dynamic Response of Beryllium," Shocked Compression of Condensed Matter, AIP Conf. Proc. 1195 833 (2009).

  16. J. M. D. Lane and A. P. Thompson, "Molecular Dynamics Simulation of Shock-Induced Phase Transformation in Germanium," Shocked Compression of Condensed Matter, AIP Conf. Proc. 1195 1157 (2009).

  17. A. A. Selezenev, A. Yu. Aleynikov, N. S. Ganchuk, P.V. Ermakov, S. N. Ganchuk, J. B. Aidun, and A. P. Thompson, "Shock Compression Calculation of RDX and PETN Molecular Crystals using Hugoniostat Method," Shocked Compression of Condensed Matter, AIP Conf. Proc. 1195 821 (2009).

    2008



  18. J. Budzien, D. R. Rottach, J. G. Curro, C. S. Lo, A. P. Thompson, "A New Constitutive Model for the Chemical Aging of Rubber Networks in Deformed States," Macromolecules, 41 9896 (2008).

  19. A. Slepoy, A. P. Thompson, S. J. Plimpton, "A Constant-Time Kinetic Monte Carlo Algorithm for Simulation of Large Biochemical Reaction Networks," J. Chem. Phys., 128 205101 (2008).

    2007



  20. A. Slepoy, M. D. Peters, and A. P. Thompson, "Searching for Globally Optimal Functional Forms for Interatomic Potentials Using Genetic Programming with Parallel Tempering," J. Comp. Chem., 28, 2465 (2007).

  21. J. Quenneville, T. C. Germann, A. P. Thompson, E. M. Kober, "Molecular dynamics studies of thermal induced chemistry in TATB," SCCM 2007, AIP CONFERENCE PROCEEDINGS, 955 451-454 (2007).

    2006



  22. A. H. Edwards, A. C. Pineda, P. A. Schultz, M. G. Martin, A. P. Thompson, H. P. Hjalmarson, C. J. Umrigar, "Electronic structure of intrinsic defects in crystalline germanium telluride," Phys. Rev. B, 73 45210 (2006).

    2005



  23. A. H. Edwards, A. C. Pineda, P. A. Schultz, M. G. Martin, A. P. Thompson, H. P. Hjalmarson, "Theory of persistent, p-type, metallic conduction in c-GeTe," J. Phys.: Cond. Mat., 17, 329-35 (2005).

    2000-2004



  24. D. Rottach, J. G. Curro, G. S. Grest and A. P. Thompson, "Effect of Strain History on Stress and Permanent Set in Crosslinking Networks: A Molecular Dynamics Study," Macromolecules, 37, 5468 (2004).

  25. M. G. Martin and A. P. Thompson, "Industrial Property Prediction using Towhee and LAMMPS," Fluid Phase Equilibria, 217 105 (2004).

  26. A. P. Thompson, "Non-equilibrium Molecular Dynamics Simulation of Electroosmotic Flow in a Charged Nanopore," J. Chem. Phys., 119, 7503 (2003).

  27. Martin, M. G., Thompson A. P., and Nenoff, T. M., "Effect of Pressure, Membrane Thickness and Placement of Control Volumes on the Flux of Methane through Thin Silicalite Membranes" J. Chem. Phys. 114, 7174 (2001).

  28. Chandross M., Webb E. B., Grest G. S., Martin M. G., Thompson A. P., and Roth M. W., "Dynamics and Exchange at Gas-Zeolite Interfaces I: Pure Component Butane and Isobutane", J. Phys. Chem. B, 105, 5700 (2001).

  29. Rallabandi P. S., Thompson A. P., Ford D. M., "A molecular modeling study of entropic and energetic selectivities in air separation with glassy polymers", Macromolecules, 33, 3142 (2000).

  30. Frink L. J. D., Thompson A. P., Salinger A. G., "Applying molecular theory to steady-state diffusing systems", J. Chem. Phys. 112, 7564, (2000).

    1995-1999



  31. Thompson, A. P. and Heffelfinger, G. S., "Direct Molecular Simulation of Gradient Driven Diffusion of Large Molecules using Constant Pressure" J. Chem. Phys. 110 10693 (1999).

  32. Thompson, A. P., Ford, D. M., and Heffelfinger, G. S., "Direct Molecular Simulation of Gradient Driven Diffusion", J. Chem. Phys., 109, 6406 (1998).

  33. Thompson, A. P. and Glandt, E. D., "Polymers in Random Porous Materials: Structure, Thermodynamics and Concentration Effects" Macromolecules, 29, 4314 (1996).

  34. Ford, D. M., Thompson, A. P., and Glandt, E. D., "Thermodynamics of Fluids in Random Microporous Materials from Scaled Particle Theory," J. Chem. Phys., 103, 1099 (1995).

    1990-1994



  35. Thompson, A. P. and Glandt, E. D., "Adsorption of Polymeric Fluids in Microporous Materials. I. Ideal Freely-jointed Chains," J. Chem. Phys., 99, 8325 (1993).

  36. Thompson, A. P., Corti, D. S., Myers, A. L. and Glandt, E. D., "Irreversible Adsorption in Porous Materials," Fundamentals of Adsorption: Proc. IVth Int. Conf. on Fundamentals of Adsorption, p. 397 (Kodansha, 1993).

  37. Thompson, A. P. and Glandt, E. D., "Low Coverage Kinetics of Correlated Sequential Adsorption," Phys. Rev. A, 46, 4639 (1992).

  38. Thompson, A. P. and Glandt, E. D., "The Length of Intersection and the Number of Cusps in Assemblies of Interpenetrating Spheres," J. Chem. Phys., 97, 1932 (1992).

  39. Thompson, A. P. and Glandt, E. D., "Random Sequential Adsorption in Porous Solids," J. Colloid Interface Sci., 146, 63 (1991).

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