Publications

Lane, James M.; Thompson, Aidan P.; Vogler, Tracy V.

Abstract not provided.

Shan, Tzu-Ray S.; Thompson, Aidan P.; Yarrington, Cole Y.; Kittell, David E.; Wixom, Ryan R.

Abstract not provided.

Yarrington, Cole Y.; Wixom, Ryan R.; Kittell, David E.; Thompson, Aidan P.; Shan, Tzu-Ray S.

Abstract not provided.

Journal of Computational Physics

Thompson, Aidan P.; Swiler, Laura P.; Trott, C.R.; Foiles, Stephen M.; Tucker, G.J.

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

Thompson, Aidan P.

The purpose of this work is to understand how defects control initiation in energetic materials used in stockpile components; Sequoia gives us the core-count to run very large-scale simulations of up to 10 million atoms and; Using an OpenMP threaded implementation of the ReaxFF package in LAMMPS, we have been able to get good parallel efficiency running on 16k nodes of Sequoia, with 1 hardware thread per core.

International Journal of High Performance Computing Applications

Levy, Scott; Ferreira, Kurt; Bridges, Patrick G.; Thompson, Aidan P.; Trott, Christian R.

Building the next-generation of extreme-scale distributed systems will require overcoming several challenges related to system resilience. As the number of processors in these systems grow, the failure rate increases proportionally. One of the most common sources of failure in large-scale systems is memory. In this paper, we propose a novel runtime for transparently exploiting memory content similarity to improve system resilience by reducing the rate at which memory errors lead to node failure. We evaluate the viability of this approach by examining memory snapshots collected from eight high-performance computing (HPC) applications and two important HPC operating systems. Based on the characteristics of the similarity uncovered, we conclude that our proposed approach shows promise for addressing system resilience in large-scale systems.

Shan, Tzu-Ray S.; Wixom, Ryan R.; Thompson, Aidan P.

Abstract not provided.

Physical Review B - Condensed Matter and Materials Physics

Lane, J.M.; Thompson, Aidan P.; Vogler, Tracy V.

Under shock compression, most porous materials exhibit lower densities for a given pressure than that of a full-dense sample of the same material. However, some porous materials exhibit an anomalous, or enhanced, densification under shock compression. We demonstrate a molecular mechanism that drives this behavior. We also present evidence from atomistic simulation that silicon belongs to this anomalous class of materials. Atomistic simulations indicate that local shear strain in the neighborhood of collapsing pores nucleates a local solid-solid phase transformation even when bulk pressures are below the thermodynamic phase transformation pressure. This metastable, local, and partial, solid-solid phase transformation, which accounts for the enhanced densification in silicon, is driven by the local stress state near the void, not equilibrium thermodynamics. This mechanism may also explain the phenomenon in other covalently bonded materials.

Thompson, Aidan P.; Schultz, Peter A.; Crozier, Paul C.; Moore, Stan G.; Swiler, Laura P.; Stephens, John A.; Trott, Christian R.; Foiles, Stephen M.; Tucker, Garritt J.

This report summarizes the result of LDRD project 12-0395, titled "Automated Algorithms for Quantum-level Accuracy in Atomistic Simulations." During the course of this LDRD, we have developed an interatomic potential for solids and liquids called Spectral Neighbor Analysis Poten- tial (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected on to a basis of hyperspherical harmonics in four dimensions. The SNAP coef- ficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. Global optimization methods in the DAKOTA software package are used to seek out good choices of hyperparameters that define the overall structure of the SNAP potential. FitSnap.py, a Python-based software pack- age interfacing to both LAMMPS and DAKOTA is used to formulate the linear regression problem, solve it, and analyze the accuracy of the resultant SNAP potential. We describe a SNAP potential for tantalum that accurately reproduces a variety of solid and liquid properties. Most significantly, in contrast to existing tantalum potentials, SNAP correctly predicts the Peierls barrier for screw dislocation motion. We also present results from SNAP potentials generated for indium phosphide (InP) and silica (SiO 2 ). We describe efficient algorithms for calculating SNAP forces and energies in molecular dynamics simulations using massively parallel computers and advanced processor ar- chitectures. Finally, we briefly describe the MSM method for efficient calculation of electrostatic interactions on massively parallel computers.

The 15th International Detonation Symposium

Shan, Tzu-Ray S.; Thompson, Aidan P.

Abstract not provided.

15th International Detonation Symposium

Shan, Tzu-Ray S.; Wixom, Ryan R.; Thompson, Aidan P.

Abstract not provided.

Shan, Tzu-Ray S.; Thompson, Aidan P.

Abstract not provided.

Shan, Tzu-Ray S.; Wixom, Ryan R.; Thompson, Aidan P.

Abstract not provided.

Trott, Christian R.; Hammond, Simon D.; Thompson, Aidan P.

Abstract not provided.

Journal of Physics: Conference Series

Thompson, Aidan P.; Shan, Tzu-Ray S.

Ammonium nitrate mixed with fuel oil (ANFO) is a commonly used blasting agent. In this paper we investigated the shock properties of pure ammonium nitrate (AN) and two different mixtures of ammonium nitrate and n-dodecane by characterizing their Hugoniot states. We simulated shock compression of pure AN and ANFO mixtures using the Multi-scale Shock Technique, and observed differences in chemical reaction. We also performed a large-scale explicit sub-threshold shock of AN crystal with a 10 nm void filled with 4.4 wt% of n-dodecane. We observed the formation of hotspots and enhanced reactivity at the interface region between AN and n-dodecane molecules.

Foiles, Stephen M.; Thompson, Aidan P.; Swiler, Laura P.; Trott, Christian R.

Abstract not provided.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Trott, Christian R.; Hammond, Simon D.; Thompson, Aidan P.

The rapidly improving compute capability of contemporary processors and accelerators is providing the opportunity for significant increases in the accuracy and fidelity of scientific calculations. In this paper we present performance studies of a new molecular dynamics (MD) potential called SNAP. The SNAP potential has shown great promise in accurately reproducing physics and chemistry not described by simpler potentials. We have developed new algorithms to exploit high single-node concurrency provided by three different classes of machine: the Titan GPU-based system operated by Oak Ridge National Laboratory, the combined Sequoia and Vulcan BlueGene/Q machines located at Lawrence Livermore National Laboratory, and the large-scale Intel Sandy Bridge system, Chama, located at Sandia. Our analysis focuses on strong scaling experiments with approximately 246,000 atoms over the range 1-122,880 nodes on Sequoia/Vulcan and 40-18,630 nodes on Titan. We compare these machine in terms of both simulation rate and power efficiency. We find that node performance correlates with power consumption across the range of machines, except for the case of extreme strong scaling, where more powerful compute nodes show greater efficiency. This study is a unique assessment of a challenging, scientifically relevant calculation running on several of the world's leading contemporary production supercomputing platforms. © 2014 Springer International Publishing.

Shan, Tzu-Ray S.; Thompson, Aidan P.; Plimpton, Steven J.

Abstract not provided.

Desjarlais, Michael P.; Thompson, Aidan P.; Brennecka, Geoffrey L.; Marinella, Matthew J.

Density-functional theory calculations, ab-initio molecular dynamics, and the Kubo-Greenwood formula are applied to predict electrical conductivity in Ta2Ox (0 x 5) as a function of composition, phase, and temperature, where additional focus is given to various oxidation states of the O monovacancy (VOn; n=0,1+,2+). Our calculations of DC conductivity at 300K agree well with experimental measurements taken on Ta2Ox thin films and bulk Ta2O5 powder-sintered pellets, although simulation accuracy can be improved for the most insulating, stoichiometric compositions. Our conductivity calculations and further interrogation of the O-deficient Ta2O5 electronic structure provide further theoretical basis to substantiate VO0 as a donor dopant in Ta2O5 and other metal oxides. Furthermore, this dopant-like behavior appears specific to neutral VO cases in both Ta2O5 and TiO2 and was not observed in other oxidation states. This suggests that reduction and oxidation reactions may effectively act as donor activation and deactivation mechanisms, respectively, for VO0 in transition metal oxides.

Thompson, Aidan P.; Trott, Christian R.; Swiler, Laura P.; Tucker, Garritt T.; Foiles, Stephen M.; Plimpton, Steven J.

Abstract not provided.

Shan, Tzu-Ray S.; Thompson, Aidan P.; Wills, Ann E.

Abstract not provided.

Thompson, Aidan P.; Schultz, Peter A.; Swiler, Laura P.; Trott, Christian R.; Tucker, Garritt T.; Foiles, Stephen M.

Abstract not provided.

Trott, Christian R.; Thompson, Aidan P.

Abstract not provided.

Proposed for publication in Jounal of Physical Chemistry A.

Thompson, Aidan P.; Shan, Tzu-Ray S.

Abstract not provided.

Ferreira, Kurt; Thompson, Aidan P.; Trott, Christian R.; Levy, Scott L.

Abstract not provided.