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 871851322
USA
Tel: +1 505 844 9702
Cell: +1 505 218 1011
Email: athompsATsandiaDOTgov
http://www.cs.sandia.gov/~athomps
Related Links
FitSNAP
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 machinelearning interatomic potentials.
Curriculum Vitae
Publications
Google Scholar
2023

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.

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.

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.

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.

J. A. Mitchell, F. F. Abdeljawad, C. C. Battaile, C. GarciaCardona, 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 onlattice kinetic and Metropolis Monte Carlo models for materials processing. Modelling and Simulation in Materials Science and Engineering, 2023.

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

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

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

J. T Willman, K. NguyenCong, 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.

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.

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 particlebased materials modeling at the atomic, meso, and continuum scales. Comp. Phys. Comm., 271:108171, 2022.
2021

K. NguyenCong, 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.

S. Nikolov, M. A. Wood, A. Cangi, J.B. Maillet, M.C. Marinica, A. P. Thompson, M. P. Desjarlais, and J. Tranchida. Datadriven magnetoelastic predictions with scalable classical spinlattice dynamics. npj Computational Materials, 7(1):1–12, 2021.

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.

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

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.

M. A. Cusentino, M. A. Wood, and A. P. Thompson,
"Berylliumdriven structural evolution at the divertor surface,"
Nuclear Fusion 61 046049 (2021).
2020

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 pressureinduced phase transition,"
Shocked Compression of Condensed Matter, AIP Conf. Proc. 2272 100016 (2020).

Jonathan T. Willman, Ashley S. Williams, Kien NguyenCong, 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).

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).

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

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).

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

M. A. Wood, M. A. Cusentino, B. D. Wirth, and A. P. Thompson,
"Datadriven material models for atomistic simulation,"
Phys. Rev. B, 99 184305 (2019).
2018

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

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).

M. A. Wood, and A. P. Thompson,
"Extending the accuracy of the SNAP interatomic potential form,"
J. Chem. Phys., 148 241721 (2018).
2017

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

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

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).

T.R. Shan, R. R. Wixom, and A. P. Thompson,
"Micronscale Reactive Atomistic Simulations of Void Collapse and Hotspot Growth in PETN,"
Proceedings 15th International Detonation Symposium ONR4328015 962 (2015).

T.R. Shan, R. R. Wixom, and A. P. Thompson,
"Nanoscale VoidEnhanced Initiation in Hexanitrostilbene,"
Proceedings 15th International Detonation Symposium ONR4328015 878 (2015).

A. P. Thompson , L.P. Swiler, C.R. Trott, S.M. Foiles, and G.J. Tucker,
"Spectral neighbor analysis method for automated generation of quantumaccurate interatomic potentials,"
J. Comp. Phys., 285 316 (2015).
2014

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

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).

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).

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

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

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

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

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).

T.R. Shan, R. R. Wixom, A. E. Mattsson, and A. P. Thompson ,
"Atomistic Simulation of Orientation Dependence in ShockInduced Initiation of Pentaerythritol Tetranitrate,"
J. Phys. Chem. B, 117 928 (2013).
2012

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

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

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).

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

S. Jayaraman, A. P. Thompson, and O. A. von Lilienfeld,
"Molten salt eutectics from atomistic simulations,"
Phys. Rev. E, 84 030201 (2011).
2010

H. Asegun, G. Chen, S. J. Plimpton, and A. P. Thompson,
"1Dto3D transition of phonon heat conduction in polyethylene using molecular dynamics simulations,"
Phys. Rev. B, 82 144308 (2010).

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 compressiveshear reaction dynamics simulations,"
Appl. Phys. Lett., 96 081918 (2010).

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

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

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

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

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

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).

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).

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

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

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).

A. Slepoy,
A. P. Thompson, S. J. Plimpton,
"A ConstantTime Kinetic Monte Carlo Algorithm for Simulation of Large
Biochemical Reaction Networks," J. Chem. Phys., 128 205101
(2008).
2007

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).

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 451454 (2007).
2006

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

A. H. Edwards, A. C. Pineda, P. A.
Schultz, M. G. Martin, A. P. Thompson,
H. P. Hjalmarson, "Theory of persistent, ptype,
metallic conduction in cGeTe," J. Phys.:
Cond. Mat., 17, 32935 (2005).
20002004

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).

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

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

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).

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

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).

Frink L. J. D., Thompson A. P.,
Salinger A. G., "Applying molecular theory to steadystate diffusing systems", J.
Chem. Phys. 112, 7564, (2000).
19951999

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).

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

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

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).
19901994

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

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).

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

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).

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