Sandia National Laboratories
OTHER SITES
Center for Computing Research
Materials Science and Engineering
Center for Integrated Nanotechnologies


Contact
Dr. Aidan P. Thompson,
Distinguished Member of Technical Staff
Multiscale Science Department, 1444
Sandia National Laboratories
PO Box 5800, Mail Stop 1322
Albuquerque, New Mexico 87185-1322
USA
Tel: +1 505 844 9702
Cell: +1 505 218 1011
E-mail: athompsATsandiaDOTgov
http://www.cs.sandia.gov/~athomps


Related Links

FitSNAP

FitSNAP

LAMMPS

LAMMPS

Aidan Thompson
I work on the development of predictive atomistic materials modeling capabilities enabled by extreme scale computing platforms. This involves both the development of more accurate interatomic potentials and also the development of better algorithms for evaluating these potentials on advanced computing platforms. I lead the development of both the LAMMPS molecular dynamics (MD) package and the FitSNAP package for training machine-learning interatomic potentials.

Curriculum Vitae

Publications

    Google Scholar

    2023



  1. M. A. Cusentino, E. L. Sikorski, M. J. McCarthy, A. P. Thompson, and M. A. Wood. Dynamic formation of preferentially lattice oriented, self trapped hydrogen clusters. Materials Research Express, 10(10):106513, 2023.

  2. M. A. Cusentino, B. Nebgen, K. M. Barros, J. S. Smith, J. D. Shimanek, A. Allen, A. P. Thompson, S. J. Fensin, and J. M. D. Lane. Molecular dynamics of high pressure tin phases: Empirical and machine learned interatomic potentials. In AIP Conference Proceedings, volume 2844. AIP Publishing, 2023.

  3. L. Fiedler, N. A. Modine, S. Schmerler, D. J. Vogel, G. A. Popoola, A. P. Thompson, S. Rajamanickam, and A. Cangi. Predicting electronic structures at any length scale with machine learning. npj Computational Materials, 9(1):115, 2023.

  4. A. Rohskopf, C. Sievers, N. Lubbers, M.A. Cusentino, J. Goff, J. Janssen, M. McCarthy, D. Montes Oca de Zapiain, S. Nikolov, K. Sargsyan, D. Sema, E. Sikorski, L. Williams, A. P. Thompson, and M.A. Wood. FitSNAP: Atomistic machine learning with LAMMPS. Journal of Open Source Software, 8(84):5118, 2023.

  5. J. A. Mitchell, F. F. Abdeljawad, C. C. Battaile, C. Garcia-Cardona, E. A. Holm, E. R. Homer, J. Madison, T. M. Rodgers, A. P. Thompson, V. Tikare, E. Webb, and S. Plimpton. Parallel simulation via SPPARKS of on-lattice kinetic and Metropolis Monte Carlo models for materials processing. Modelling and Simulation in Materials Science and Engineering, 2023.

  6. S. Nikolov, P. Nieves, A. P. Thompson, M. A. Wood, and J. Tranchida. Temperature dependence of magnetic anisotropy and magnetoelasticity from classical spin-lattice calculations. Physical Review B, 107(9):094426, 2023.

  7. E. L. Sikorski, M. A. Cusentino, M. J. McCarthy, J. Tranchida, M. A. Wood, and A. P. Thompson. Machine learned interatomic potential for dispersion strengthened plasma facing components. The Journal of Chemical Physics, 158(11), 2023.

    2022



  8. G. Clavier and A. P. Thompson. Computation of the thermal elastic constants for arbitrary manybody potentials in lammps using the stress-fluctuation formalism.

  9. J. T Willman, K. Nguyen-Cong, A. S. Williams, A. B. Belonoshko, S. G. Moore, A. P. Thompson, M. A. Wood, and I. I. Oleynik. Machine learning interatomic potential for simulations of carbon at extreme conditions. Physical Review B, 106(18):L180101, 2022.

  10. D. Montes de Oca Zapiain, M. A Wood, N. Lubbers, C. Z. Pereyra, A. P. Thompson, and D. Perez. Training data selection for accuracy and transferability of interatomic potentials. npj Computational Materials, 8(1):189, 2022.

  11. A. P. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in ’t Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott, and S. J. Plimpton. LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comp. Phys. Comm., 271:108171, 2022.

    2021



  12. K. Nguyen-Cong, J. T. Willman, Stan G. Moore, A. B. Belonoshko, R. Gayatri, E. Weinberg, M. A. Wood, A. P. Thompson, and I. I. Oleynik. Billion atom molecular dynamics simulations of carbon at extreme conditions and experimental time and length scales. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, Gordon Bell Finalist, SC ’21, New York, NY, USA, 2021. Association for Computing Machinery.

  13. S. Nikolov, M. A. Wood, A. Cangi, J.-B. Maillet, M.-C. Marinica, A. P. Thompson, M. P. Desjarlais, and J. Tranchida. Data-driven magneto-elastic predictions with scalable classical spin-lattice dynamics. npj Computational Materials, 7(1):1–12, 2021.

  14. Y. Lysogorskiy, C. van der Oord, A. Bochkarev, S. Menon, M. Rinaldi, T. Hammerschmidt, M. Mrovec, A. P. Thompson, G. Csanyi, C. Ortner, and R. Drautz. Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon. npj Computational Materials, 7(1):97, 2021.

  15. J. A. Ellis, L. Fiedler, G. A. Popoola, N. A. Modine, J. A. Stephens, A. P. Thompson, A. Cangi, and S. Rajamanickam. Accelerating finite-temperature Kohn-Sham density functional theory with deep neural networks. Phys. Rev. B, 104:035120, Jul 2021.

  16. R. Gayatri, S. Moore, E. Weinberg, N. Lubbers, S. Anderson, J. Deslippe, D. Perez, and A. P. Thompson. Rapid exploration of optimization strategies on advanced architectures using testsnap and lammps. arXiv preprint, 2021.

  17. M. A. Cusentino, M. A. Wood, and A. P. Thompson, "Beryllium-driven structural evolution at the divertor surface," Nuclear Fusion 61 046049 (2021).

    2020



  18. J. M. D. Lane, A. P. Thompson, I. Srivastava, G. S. Grest, T. Ao, B. Stoltzfus, K. Austin, H. Fan, D. Morgan, and M. D. Knudson, "Scale and rate in CdS pressure-induced phase transition," Shocked Compression of Condensed Matter, AIP Conf. Proc. 2272 100016 (2020).

  19. Jonathan T. Willman, Ashley S. Williams, Kien Nguyen-Cong, A. P. Thompson, Mitchell A. Wood, Anatoly B. Belonoshko, and Ivan I. Oleynik, "Quantum accurate snap carbon potential for MD shock simulations," Shocked Compression of Condensed Matter, AIP Conf. Proc. 2272 070055 (2020).

  20. M. A. Cusentino, M. A. Wood, and A. P. Thompson, "Suppression of helium bubble nucleation in beryllium exposed tungsten surfaces," Nuclear Fusion, 60 126018 (2020).

  21. A. Tran, J. Tranchida, T. Wildey, and A. P. Thompson, "Multi-fidelity machine- learning with uncertainty quantification and bayesian optimization for materials design: Application to ternary random alloys." J. Chem. Phys., 153 074705 (2020).

  22. M. A. Cusentino, M. A. Wood, and A. P. Thompson, "Explicit multielement extension of the spectral neighbor analysis potential for chemically complex systems," J. Phys. Chem. A, 124 5456 (2020).

  23. Y. Zuo, C. Chen, X. Li, Z. Deng, Y. Chen, J. Behler, G. Csanyi, A. V. Shapeev, A. P. Thompson, M. A. Wood, and S. P. Ong, "A performance and cost assessment of machine learning interatomic potentials," J. Phys. Chem. A, 124 731 (2020).

    2019



  24. M. A. Wood, M. A. Cusentino, B. D. Wirth, and A. P. Thompson, "Data-driven material models for atomistic simulation," Phys. Rev. B, 99 184305 (2019).

    2018



  25. J. M. D. Lane , K. Leung, A. P. Thompson, and M. E Cuneo, "Water desorption from rapidly-heated metal oxide surfaces-first principles, molecular dynamics, and the Temkin isotherm," J. Phys.: Condens. Matter, 30 465002 (2018).

  26. J. Tranchida, S. J. Plimpton, P. Thibaudeau, and A. P. Thompson, "Massively parallel symplectic algorithm for coupled magnetic spin dynamics and molecular dynamics," J. Comp. Phys., 148 241721 (2018).

  27. M. A. Wood, and A. P. Thompson, "Extending the accuracy of the SNAP interatomic potential form," J. Chem. Phys., 148 241721 (2018).

    2017



  28. M. A. Wood, D. E. Kittell, C. D. Yarrington, and A. P. Thompson, "Multiscale modeling of shock wave localization in porous energetic material," Phys. Rev. B, 97 014109 (2017).

    2016



  29. T. R. Shan, R. R. Wixom and A. P. Thompson, "Extended asymmetric hot region formation due to shockwave interactions following void collapse in shocked high explosive," Phys. Rev. B, 94 054308 (2016).

    2015



  30. J. M. D. Lane, A. P. Thompson, and T. J. Vogler, "Enhanced densification, strength and molecular mechanisms in shock compressed porous silicon," Shocked Compression of Condensed Matter, AIP Conf. Proc. 1793 120010 (2017).

  31. T.-R. Shan, R. R. Wixom, and A. P. Thompson, "Micron-scale Reactive Atomistic Simulations of Void Collapse and Hotspot Growth in PETN," Proceedings 15th International Detonation Symposium ONR-43-280-15 962 (2015).

  32. T.-R. Shan, R. R. Wixom, and A. P. Thompson, "Nanoscale Void-Enhanced Initiation in Hexanitrostilbene," Proceedings 15th International Detonation Symposium ONR-43-280-15 878 (2015).

  33. A. P. Thompson , L.P. Swiler, C.R. Trott, S.M. Foiles, and G.J. Tucker, "Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials," J. Comp. Phys., 285 316 (2015).

    2014



  34. C.R. Trott, S.D. Hammond, A. P. Thompson, "SNAP: Strong scaling high fidelity molecular dynamics simulations on leadership-class computing platforms," Supercomputing, (Lecture Notes in Computer Science), 8488 19 (2014).

  35. J.M.D. Lane, A. P. Thompson, and T.J. Vogler, "Enhanced densification under shock compression in porous silicon," Phys. Rev. B, 90 134311 (2014).

  36. S. Levy, K. B. Ferreira, P. G. Bridges A. P. Thompson , and C. R. Trott, "Evaluating the Feasibility of Using Memory Content Similarity to Improve System Resilience," International Journal of High Performance Computing, 28 11 (2014).

  37. T. Shan and A. P. Thompson , "Shock-induced hotspot formation and chemical reaction initiation in PETN containing a spherical void," Journal of Physics: Conference Series 500 172009 (2014).

  38. A. P. Thompson , and T. Shan, "Reactive atomistic simulations of shock-induced initiation processes in mixtures of ammonium nitrate and fuel oil," Journal of Physics: Conference Series 500 052046 (2014).

  39. T. Shan, A. C. T. van Duin, A. P. Thompson , "Development of a ReaxFF Reactive Force Field for Ammonium Nitrate and Application to Shock Hugoniots, " J. Phys. Chem. A, 118 (2014).

    2013



  40. R. J. Bondi, M. P. Desjarlais, A. P. Thompson , G. L. Brennecka, and M. J. Marinella, "Electrical conductivity in oxygen-deficient phases of tantalum pentoxide from first-principles calculations," J. Appl. Phys., 114 203701 (2013).

  41. S. Root, T. A. Haill, J. M. D. Lane, A. P. Thompson , G. S. Grest, D. G. Schroen, and T. R. Mattsson, "Shock compression of hydrocarbon foam to 200 GPa: Experiments, atomistic simulations, and mesoscale hydrodynamic modeling," J. Appl. Phys., 114 103502 (2013).

  42. 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



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

  44. 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).

  45. 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).

  46. 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



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

    2010



  48. 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).

  49. 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).

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

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

  52. 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).

  53. 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



  54. 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).

  55. 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).

  56. 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).

  57. 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).

  58. 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



  59. 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).

  60. 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



  61. 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).

  62. 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



  63. 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



  64. 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



  65. 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).

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

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

  68. 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).

  69. 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).

  70. 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).

  71. 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



  72. 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).

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

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

  75. 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



  76. 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).

  77. 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).

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

  79. 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).

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

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