Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials. Program Summary: Program Title: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) CPC Library link to program files: https://doi.org/10.17632/cxbxs9btsv.1 Developer's repository link: https://github.com/lammps/lammps Licensing provisions: GPLv2 Programming language: C++, Python, C, Fortran Supplementary material: https://www.lammps.org Nature of problem: Many science applications in physics, chemistry, materials science, and related fields require parallel, scalable, and efficient generation of long, stable classical particle dynamics trajectories. Within this common problem definition, there lies a great diversity of use cases, distinguished by different particle interaction models, external constraints, as well as timescales and lengthscales ranging from atomic to mesoscale to macroscopic. Solution method: The LAMMPS code uses parallel spatial decomposition, distributed neighbor lists, and parallel FFTs for long-range Coulombic interactions [1]. The time integration algorithm is based on the Størmer-Verlet symplectic integrator [2], which provides better stability than higher-order non-symplectic methods. In addition, LAMMPS supports a wide range of interatomic potentials, constraints, diagnostics, software interfaces, and pre- and post-processing features. Additional comments including restrictions and unusual features: This paper serves as the definitive reference for the LAMMPS code. References: [1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117 (1995) 1–19. [2] L. Verlet, Computer experiments on classical fluids: I. Thermodynamical properties of Lennard–Jones molecules, Phys. Rev. 159 (1967) 98–103.
Sprague, Michael S.; Ananthan, Shreyas A.; Gruchalla, Kenny G.; lawson, michael j.; Rood, Jon R.; Swirydowicz, K.S.; Thomas, Steve T.; Vijayakumar, Ganesh V.; Crozier, Paul C.; Dohrmann, Clark R.; Hu, Jonathan J.; Williams, Alan B.; Turner, John A.; Prokopenko, A.P.; Moser, Robert M.; Melvin, J.M.
The SPARC (Sandia Parallel Aerodynamics and Reentry Code) will provide nuclear weapon qualification evidence for the random vibration and thermal environments created by re-entry of a warhead into the earth’s atmosphere. SPARC incorporates the innovative approaches of ATDM projects on several fronts including: effective harnessing of heterogeneous compute nodes using Kokkos, exascale-ready parallel scalability through asynchronous multi-tasking, uncertainty quantification through Sacado integration, implementation of state-of-the-art reentry physics and multiscale models, use of advanced verification and validation methods, and enabling of improved workflows for users. SPARC is being developed primarily for the Department of Energy nuclear weapon program, with additional development and use of the code is being supported by the Department of Defense for conventional weapons programs.
This report evaluates several interpolants implemented in the Digital Image Correlation Engine (DICe), an image correlation software package developed by Sandia. By interpolants we refer to the basis functions used to represent discrete pixel intensity data as a continuous signal. Interpolation is used to determine intensity values in an image at non - pixel locations. It is also used, in some cases, to evaluate the x and y gradients of the image intensities. Intensity gradients subsequently guide the optimization process. The goal of this report is to inform analysts as to the characteristics of each interpolant and provide guidance towards the best interpolant for a given dataset. This work also serves as an initial verification of each of the interpolants implemented.
Computational science and engineering application programs are typically large, complex, and dynamic, and are often constrained by distribution limitations. As a means of making tractable rapid explorations of scientific and engineering application programs in the context of new, emerging, and future computing architectures, a suite of "miniapps" has been created to serve as proxies for full scale applications. Each miniapp is designed to represent a key performance characteristic that does or is expected to significantly impact the runtime performance of an application program. In this paper we introduce a methodology for assessing the ability of these miniapps to effectively represent these performance issues. We applied this methodology to three miniapps, examining the linkage between them and an application they are intended to represent. Herein we evaluate the fidelity of that linkage. This work represents the initial steps required to begin to answer the question, "Under what conditions does a miniapp represent a key performance characteristic in a full app?"
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.