Publications

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Peridynamics is a nonlocal formulation of continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamic model. This document details the implementation of a discrete peridynamic model within the LAMMPS molecular dynamic code. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized, and overviews the LAMMPS implementation. A nontrivial example problem is also included.

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Cities without an early warning system of indwelling sensors can consider monitoring their networks manually, especially during times of heightened security levels. We consider the problem of calculating an optimal schedule for manual sampling in a municipal water network. Preliminary computations with a small-scale example indicate that during normal times, manual sampling can provide some benefit, but it is far inferior to an indwelling sensor network. However, given information that significantly constrains the nature of an imminent threat, manual sampling can perform as well as a small sensor network designed to handle normal threats. Copyright ASCE 2006.

We present an LES-type variational multiscale theory of turbulence. Our approach derives completely from the incompressible Navier-Stokes equations and does not employ any ad hoc devices, such as eddy viscosities. We tested the formulation on forced homogeneous isotropic turbulence and turbulent channel flows. In the calculations, we employed linear, quadratic and cubic NURBS. A dispersion analysis of simple model problems revealed NURBS elements to be superior to classical finite elements in approximating advective and diffusive processes, which play a significant role in turbulence computations. The numerical results are very good and confirm the viability of the theoretical framework. © 2007 Elsevier B.V. All rights reserved.

Partitioned global address space (PGAS) programming models have been identified as one of the few viable approaches for dealing with emerging many-core systems. These models tend to generate many small messages, which requires specific support from the network interface hardware to enable efficient execution. In the past, Cray included E-registers on the Cray T3E to support the SHMEM API; however, with the advent of multi-core processors, the balance of computation to communication capabilities has shifted toward computation. This paper explores the message rates that are achievable with multi-core processors and simplified PGAS support on a more conventional network interface. For message rate tests, we find that simple network interface hardware is more than sufficient. We also find that even typical data distributions, such as cyclic or block-cyclic, do not need specialized hardware support. Finally, we assess the impact of such support on the well known RandomAccess benchmark. (c) 2007 ACM.

In this paper, we introduce EXACT, the EXperimental Algorithmics Computational Toolkit. EXACT is a software framework for describing, controlling, and analyzing computer experiments. It provides the experimentalist with convenient software tools to ease and organize the entire experimental process, including the description of factors and levels, the design of experiments, the control of experimental runs, the archiving of results, and analysis of results. As a case study for EXACT, we describe its interaction with FAST, the Sandia Framework for Agile Software Testing. EXACT and FAST now manage the nightly testing of several large software projects at Sandia. We also discuss EXACT's advanced features, which include a driver module that controls complex experiments such as comparisons of parallel algorithms. Copyright 2007 ACM.

Recently, extensive focus has been placed on determining the optimal locations of sensors within a distribution system to minimize the impact on public health from intentional intrusion events. Modified versions of these tools may have additional benefits for determining monitoring locations for other more common objectives associated with distribution systems. A modified Sensor Placement Optimization Tool (SPOT) is presented that can be used for satisfying more generic location problems such as determining monitoring locations for tracer tests or disinfectant byproduct sampling. The utility for the modified SPOT algorithm is discussed with respect to implementing a distribution system field-scale tracer study. © 2007 ASCE.

Since the first vector supercomputers in the mid-1970's, the largest scale applications have traditionally been floating point oriented numerical codes, which can be broadly characterized as the simulation of physics on a computer. Supercomputer architectures have evolved to meet the needs of those applications. Specifically, the computational work of the application tends to be floating point oriented, and the decomposition of the problem two or three dimensional. Today, an emerging class of critical applications may change those assumptions: they are combinatorial in nature, integer oriented, and irregular. The performance of both classes of applications is dominated by the performance of the memory system. This paper compares the memory performance sensitivity of both traditional and emerging HPC applications, and shows that the new codes are significantly more sensitive to memory latency and bandwidth than their traditional counterparts. Additionally, these codes exhibit lower base-line performance, which only exacerbates the problem. As a result, the construction of future supercomputer architectures to support these applications will most likely be different from those used to support traditional codes. Quantitatively understanding the difference between the two workloads will form the basis for future design choices. ©2007 IEEE.

The extended Finite Element Method (X-FEM) is a finite-element based discretization technique developed originally to model dynamic crack propagation [1]. Since that time the method has been used for modeling physics ranging from static meso-scale material failure to dendrite growth. Here we adapt the recent advances of Vitali and Benson [2] and Song et. al. [3] to model dynamic loading of a polycry stalline material. We use demonstration problems to examine the method's efficacy for modeling the dynamic response of polycrystalline materials at the meso-scale. Specifically, we use the X-FEM to model grain boundaries. This approach allows us to i) eliminate ad-hoc mixture rules for multi-material elements and ii) avoid explicitly meshing grain boundaries. © 2007 American Institute of Physics.

Molecular dynamics and other molecular simulation methods rely on a potential energy function, based only on the relative coordinates of the atomic nuclei. Such a function, called a force field, approximately represents the electronic structure interactions of a condensed matter system. Developing such approximate functions and fitting their parameters remains an arduous, time-consuming process, relying on expert physical intuition. To address this problem, a functional programming methodology was developed that may enable automated discovery of entirely new force-field functional forms, while simultaneously fitting parameter values. The method uses a combination of genetic programming, Metropolis Monte Carlo importance sampling and parallel tempering, to efficiently search a large space of candidate functional forms and parameters. The methodology was tested using a nontrivial problem with a well-defined globally optimal solution: a small set of atomic configurations was generated and the energy of each configuration was calculated using the Lennard-Jones pair potential. Starting with a population of random functions, our fully automated, massively parallel implementation of the method reproducibly discovered the original Lennard-Jones pair potential by searching for several hours on 100 processors, sampling only a minuscule portion of the total search space. This result indicates that, with further improvement, the method may be suitable for unsupervised development of more accurate force fields with completely new functional forms. © 2007 Wiley Periodicals, Inc.

This paper presents the conceptual framework that is being used to define quantification of margins and uncertainties (QMU) for application in the nuclear weapons (NW) work conducted at Sandia National Laboratories. The conceptual framework addresses the margins and uncertainties throughout the NW life cycle and includes the definition of terms related to QMU and to figures of merit. Potential applications of QMU consist of analyses based on physical data and on modeling and simulation. Appendix A provides general guidelines for addressing cases in which significant and relevant physical data are available for QMU analysis. Appendix B gives the specific guidance that was used to conduct QMU analyses in cycle 12 of the annual assessment process. Appendix C offers general guidelines for addressing cases in which appropriate models are available for use in QMU analysis. Appendix D contains an example that highlights the consequences of different treatments of uncertainty in model-based QMU analyses.

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This work describes the convergence analysis of a Smolyak-type sparse grid stochastic collocation method for the approximation of statistical quantities related to the solution of partial differential equations with random coefficients and forcing terms (input data of the model). To compute solution statistics, the sparse grid stochastic collocation method uses approximate solutions, produced here by finite elements, corresponding to a deterministic set of points in the random input space. This naturally requires solving uncoupled deterministic problems and, as such, the derived strong error estimates for the fully discrete solution are used to compare the computational efficiency of the proposed method with the Monte Carlo method. Numerical examples illustrate the theoretical results and are used to compare this approach with several others, including the standard Monte Carlo.

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Niobium doped Lead Zirconate Titanate (PZT) with a Zr/Ti ratio of 95/5 (i.e., PZT 95/5-2Nb) is a ferroelectric with a rhombohedral structure at room temperature. A crystal (or a subdomain within a crystal) exhibits a spontaneous polarization in any one of eight crystallographically equivalent directions. Such a material becomes polarized when subjected to a large electric field. When the electric field is removed, a remanent polarization remains and a bound charge is stored. A displacive phase transition from a rhombohedral ferroelectric phase to an orthorhombic anti-ferroelectric phase can be induced with the application of a mechanical load. When this occurs, the material becomes depoled and the bound charge is released. The polycrystalline character of PZT 95/5-2Nb leads to highly non-uniform fields at the grain scale. These local fields lead to very complex material behavior during mechanical depoling that has important implications to device design and performance. This paper presents a microstructurally based numerical model that describes the 3D non-linear behavior of ferroelectric ceramics. The model resolves the structure of polycrystals directly in the topology of the problem domain and uses the extended finite element method (X-FEM) to solve the governing equations of electromechanics. The material response is computed from anisotropic single crystal constants and the volume fractions of the various polarization variants (i.e., three variants for rhombohedral anti-ferroelectric and eight for rhomobohedral ferroelectric ceramic). Evolution of the variant volume fractions is governed by the minimization of internally stored energy and accounts for ferroelectric and ferroelastic domain switching and phase transitions in response to the applied loads. The developed model is used to examine hydrostatic depoling in PZT 95/5-2Nb.

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