Publications

Atomic cluster expansion (ACE) methods provide a systematic way to describe particle local environments of arbitrary body order. For practical applications it is often required that the basis of cluster functions be symmetrized with respect to rotations and permutations. Existing methodologies yield sets of symmetrized functions that are over-complete. These methodologies thus require an additional numerical procedure, such as singular value decomposition (SVD), to eliminate redundant functions. In this work, it is shown that analytical linear relationships for subsets of cluster functions may be derived using recursion and permutation properties of generalized Wigner symbols. From these relationships, subsets (blocks) of cluster functions can be selected such that, within each block, functions are guaranteed to be linearly independent. It is conjectured that this block-wise independent set of permutation-adapted rotation and permutation invariant (PA-RPI) functions forms a complete, independent basis for ACE. Along with the first analytical proofs of block-wise linear dependence of ACE cluster functions and other theoretical arguments, numerical results are offered to demonstrate this. The utility of the method is demonstrated in the development of an ACE interatomic potential for tantalum. Using the new basis functions in combination with Bayesian compressive sensing sparse regression, some high degree descriptors are observed to persist and help achieve high-accuracy models.

Tabulated chemistry models are widely used to simulate large-scale turbulent fires in applications including energy generation and fire safety. Tabulation via piecewise Cartesian interpolation suffers from the curse-of-dimensionality, leading to a prohibitive exponential growth in parameters and memory usage as more dimensions are considered. Artificial neural networks (ANNs) have attracted attention for constructing surrogates for chemistry models due to their ability to perform high-dimensional approximation. However, due to well-known pathologies regarding the realization of suboptimal local minima during training, in practice they do not converge and provide unreliable accuracy. Partition of unity networks (POUnets) are a recently introduced family of ANNs which preserve notions of convergence while performing high-dimensional approximation, discovering a mesh-free partition of space which may be used to perform optimal polynomial approximation. We assess their performance with respect to accuracy and model complexity in reconstructing unstructured flamelet data representative of nonadiabatic pool fire models. Our results show that POUnets can provide the desirable accuracy of classical spline-based interpolants with the low memory footprint of traditional ANNs while converging faster to significantly lower errors than ANNs. For example, we observe POUnets obtaining target accuracies in two dimensions with 40 to 50 times less memory and roughly double the compression in three dimensions. We also address the practical matter of efficiently training accurate POUnets by studying convergence over key hyperparameters, the impact of partition/basis formulation, and the sensitivity to initialization.

Astra, deployed in 2018, was the first petascale supercomputer to utilize processors based on the ARM instruction set. The system was also the first under Sandia's Vanguard program which seeks to provide an evaluation vehicle for novel technologies that with refinement could be utilized in demanding, large-scale HPC environments. In addition to ARM, several other important first-of-a-kind developments were used in the machine, including new approaches to cooling the datacenter and machine. This article documents our experiences building a power measurement and control infrastructure for Astra. While this is often beyond the control of users today, the accurate measurement, cataloging, and evaluation of power, as our experiences show, is critical to the successful deployment of a large-scale platform. While such systems exist in part for other architectures, Astra required new development to support the novel Marvell ThunderX2 processor used in compute nodes. In addition to documenting the measurement of power during system bring up and for subsequent on-going routine use, we present results associated with controlling the power usage of the processor, an area which is becoming of progressively greater interest as data centers and supercomputing sites look to improve compute/energy efficiency and find additional sources for full system optimization.

An ordinary state-based peridynamic material model is proposed for single-sheet graphene. The model is calibrated using coarse-grained molecular dynamics simulations. The coarse-graining method allows the dependence of bond force on bond length to be determined, including the horizon. The peridynamic model allows the horizon to be rescaled, providing a multiscale capability and allowing for substantial reductions in computational cost compared with molecular dynamics. The calibrated peridynamic model is compared to experimental data on the deflection and perforation of a graphene sheet by an atomic force microscope probe.

We propose primal–dual mesh optimization algorithms that overcome shortcomings of the standard algorithm while retaining some of its desirable features. “Hodge-Optimized Triangulations” defines the “HOT energy” as a bound on the discretization error of the diagonalized Delaunay Hodge star operator. HOT energy is a natural choice for an objective function, but unstable for both mathematical and algorithmic reasons: it has minima for collapsed edges, and its extrapolation to non-regular triangulations is inaccurate and has unbounded minima. We propose a different extrapolation with a stronger theoretical foundation, and avoid extrapolation by recalculating the objective just beyond the flip threshold. We propose new objectives, based on normalizations of the HOT energy, with barriers to edge collapses and other undesirable configurations. We propose mesh improvement algorithms coupling these. When HOT optimization nearly collapses an edge, we actually collapse the edge. Otherwise, we use the barrier objective to update positions and weights and remove vertices. By combining discrete connectivity changes with continuous optimization, we more fully explore the space of possible meshes and obtain higher quality solutions.

The ground truth program used simulations as test beds for social science research methods. The simulations had known ground truth and were capable of producing large amounts of data. This allowed research teams to run experiments and ask questions of these simulations similar to social scientists studying real-world systems, and enabled robust evaluation of their causal inference, prediction, and prescription capabilities. We tested three hypotheses about research effectiveness using data from the ground truth program, specifically looking at the influence of complexity, causal understanding, and data collection on performance. We found some evidence that system complexity and causal understanding influenced research performance, but no evidence that data availability contributed. The ground truth program may be the first robust coupling of simulation test beds with an experimental framework capable of teasing out factors that determine the success of social science research.

We present EASEE (Edge Advertisements into Snapshots using Evolving Expectations) for partitioning streaming communication data into static graph snapshots. Given streaming communication events (A talks to B), EASEE identifies when events suffice for a static graph (a snapshot). EASEE uses combinatorial statistical models to adaptively find when a snapshot is stable, while watching for significant data shifts - indicating a new snapshot should begin. If snapshots are not found carefully, they poorly represent the underlying data - and downstream graph analytics fail: We show a community detection example. We demonstrate EASEE's strengths against several real-world datasets, and its accuracy against known-answer synthetic datasets. Synthetic datasets' results show that (1) EASEE finds known-answer data shifts very quickly; and (2) ignoring these shifts drastically affects analytics on resulting snapshots. We show that previous work misses these shifts. Further, we evaluate EASEE against seven real-world datasets (330 K to 2.5B events), and find snapshot-over-time behaviors missed by previous works. Finally, we show that the resulting snapshots' measured properties (e.g., graph density) are altered by how snapshots are identified from the communication event stream. In particular, EASEE's snapshots do not generally 'densify' over time, contradicting previous influential results that used simpler partitioning methods.

Physics-constrained machine learning is emerging as an important topic in the field of machine learning for physics. One of the most significant advantages of incorporating physics constraints into machine learning methods is that the resulting model requires significantly less data to train. By incorporating physical rules into the machine learning formulation itself, the predictions are expected to be physically plausible. Gaussian process (GP) is perhaps one of the most common methods in machine learning for small datasets. In this paper, we investigate the possibility of constraining a GP formulation with monotonicity on three different material datasets, where one experimental and two computational datasets are used. The monotonic GP is compared against the regular GP, where a significant reduction in the posterior variance is observed. The monotonic GP is strictly monotonic in the interpolation regime, but in the extrapolation regime, the monotonic effect starts fading away as one goes beyond the training dataset. Imposing monotonicity on the GP comes at a small accuracy cost, compared to the regular GP. The monotonic GP is perhaps most useful in applications where data are scarce and noisy, and monotonicity is supported by strong physical evidence.

We study both conforming and non-conforming versions of the practical DPG method for the convection-reaction problem. We determine that the most common approach for DPG stability analysis - construction of a local Fortin operator - is infeasible for the convection-reaction problem. We then develop a line of argument based on a direct proof of discrete stability; we find that employing a polynomial enrichment for the test space does not suffice for this purpose, motivating the introduction of a (two-element) subgrid mesh. The argument combines mathematical analysis with numerical experiments.

Measures of simulation model complexity generally focus on outputs; we propose measuring the complexity of a model’s causal structure to gain insight into its fundamental character. This article introduces tools for measuring causal complexity. First, we introduce a method for developing a model’s causal structure diagram, which characterises the causal interactions present in the code. Causal structure diagrams facilitate comparison of simulation models, including those from different paradigms. Next, we develop metrics for evaluating a model’s causal complexity using its causal structure diagram. We discuss cyclomatic complexity as a measure of the intricacy of causal structure and introduce two new metrics that incorporate the concept of feedback, a fundamental component of causal structure. The first new metric introduced here is feedback density, a measure of the cycle-based interconnectedness of causal structure. The second metric combines cyclomatic complexity and feedback density into a comprehensive causal complexity measure. Finally, we demonstrate these complexity metrics on simulation models from multiple paradigms and discuss potential uses and interpretations. These tools enable direct comparison of models across paradigms and provide a mechanism for measuring and discussing complexity based on a model’s fundamental assumptions and design.

Advanced finite-element discretizations and preconditioners for models of poroelasticity have attracted significant attention in recent years. The equations of poroelasticity offer significant challenges in both areas, due to the potentially strong coupling between unknowns in the system, saddle-point structure, and the need to account for wide ranges of parameter values, including limiting behavior such as incompressible elasticity. This paper was motivated by an attempt to develop monolithic multigrid preconditioners for the discretization developed in [C. Rodrigo et al., Comput. Methods App. Mech. Engrg, 341 (2018), pp. 467-484]; we show here why this is a difficult task and, as a result, we modify the discretization in [Rodrigo et al.] through the use of a reduced-quadrature approximation, yielding a more “solver-friendly” discretization. Local Fourier analysis is used to optimize parameters in the resulting monolithic multigrid method, allowing a fair comparison between the performance and costs of methods based on Vanka and Braess-Sarazin relaxation. Numerical results are presented to validate the local Fourier analysis predictions and demonstrate efficiency of the algorithms. Finally, a comparison to existing block-factorization preconditioners is also given.

Partitioned methods allow one to build a simulation capability for coupled problems by reusing existing single-component codes. In so doing, partitioned methods can shorten code development and validation times for multiphysics and multiscale applications. In this work, we consider a scenario in which one or more of the “codes” being coupled are projection-based reduced order models (ROMs), introduced to lower the computational cost associated with a particular component. We simulate this scenario by considering a model interface problem that is discretized independently on two non-overlapping subdomains. We then formulate a partitioned scheme for this problem that allows the coupling between a ROM “code” for one of the subdomains with a finite element model (FEM) or ROM “code” for the other subdomain. The ROM “codes” are constructed by performing proper orthogonal decomposition (POD) on a snapshot ensemble to obtain a low-dimensional reduced order basis, followed by a Galerkin projection onto this basis. The ROM and/or FEM “codes” on each subdomain are then coupled using a Lagrange multiplier representing the interface flux. To partition the resulting monolithic problem, we first eliminate the flux through a dual Schur complement. Application of an explicit time integration scheme to the transformed monolithic problem decouples the subdomain equations, allowing their independent solution for the next time step. We show numerical results that demonstrate the proposed method’s efficacy in achieving both ROM-FEM and ROM-ROM coupling.

National security applications require artificial neural networks (ANNs) that consume less power, are fast and dynamic online learners, are fault tolerant, and can learn from unlabeled and imbalanced data. We explore whether two fundamentally different, traditional learning algorithms from artificial intelligence and the biological brain can be merged. We tackle this problem from two directions. First, we start from a theoretical point of view and show that the spike time dependent plasticity (STDP) learning curve observed in biological networks can be derived using the mathematical framework of backpropagation through time. Second, we show that transmission delays, as observed in biological networks, improve the ability of spiking networks to perform classification when trained using a backpropagation of error (BP) method. These results provide evidence that STDP could be compatible with a BP learning rule. Combining these learning algorithms will likely lead to networks more capable of meeting our national security missions.

Abstract: Due to a beneficial balance of computational cost and accuracy, real-time time-dependent density-functional theory has emerged as a promising first-principles framework to describe electron real-time dynamics. Here we discuss recent implementations around this approach, in particular in the context of complex, extended systems. Results include an analysis of the computational cost associated with numerical propagation and when using absorbing boundary conditions. We extensively explore the shortcomings for describing electron–electron scattering in real time and compare to many-body perturbation theory. Modern improvements of the description of exchange and correlation are reviewed. In this work, we specifically focus on the Qb@ll code, which we have mainly used for these types of simulations over the last years, and we conclude by pointing to further progress needed going forward. Graphical abstract: [Figure not available: see fulltext.].

Kinetic gas dynamics in rarefied and moderate-density regimes have complex behavior associated with collisional processes. These processes are generally defined by convolution integrals over a high-dimensional space (as in the Boltzmann operator), or require evaluating complex auxiliary variables (as in Rosenbluth potentials in Fokker-Planck operators) that are challenging to implement and computationally expensive to evaluate. In this work, we develop a data-driven neural network model that augments a simple and inexpensive BGK collision operator with a machine-learned correction term, which improves the fidelity of the simple operator with a small overhead to overall runtime. The composite collision operator has a tunable fidelity and, in this work, is trained using and tested against a direct-simulation Monte-Carlo (DSMC) collision operator.

In this article, we present a general methodology to combine the Discontinuous Petrov–Galerkin (DPG) method in space and time in the context of methods of lines for transient advection–reaction problems. We first introduce a semidiscretization in space with a DPG method redefining the ideas of optimal testing and practicality of the method in this context. Then, we apply the recently developed DPG-based time-marching scheme, which is of exponential-type, to the resulting system of Ordinary Differential Equations (ODEs). We also discuss how to efficiently compute the action of the exponential of the matrix coming from the space semidiscretization without assembling the full matrix. Finally, we verify the proposed method for 1D+time advection–reaction problems showing optimal convergence rates for smooth solutions and more stable results for linear conservation laws comparing to the classical exponential integrators.

Integrated computational materials engineering (ICME) models have been a crucial building block for modern materials development, relieving heavy reliance on experiments and significantly accelerating the materials design process. However, ICME models are also computationally expensive, particularly with respect to time integration for dynamics, which hinders the ability to study statistical ensembles and thermodynamic properties of large systems for long time scales. To alleviate the computational bottleneck, we propose to model the evolution of statistical microstructure descriptors as a continuous-time stochastic process using a non-linear Langevin equation, where the probability density function (PDF) of the statistical microstructure descriptors, which are also the quantities of interests (QoIs), is modeled by the Fokker-Planck equation. We discuss how to calibrate the drift and diffusion terms of the Fokker-Planck equation from the theoretical and computational perspectives. The calibrated Fokker-Planck equation can be used as a stochastic reduced-order model to simulate the microstructure evolution of statistical microstructure descriptors PDF. Considering statistical microstructure descriptors in the microstructure evolution as QoIs, we demonstrate our proposed methodology in three integrated computational materials engineering (ICME) models: kinetic Monte Carlo, phase field, and molecular dynamics simulations.

Spin–orbit effects, inherent to electrons confined in quantum dots at a silicon heterointerface, provide a means to control electron spin qubits without the added complexity of on-chip, nanofabricated micromagnets or nearby coplanar striplines. Here, we demonstrate a singlet–triplet qubit operating mode that can drive qubit evolution at frequencies in excess of 200 MHz. This approach offers a means to electrically turn on and off fast control, while providing high logic gate orthogonality and long qubit dephasing times. We utilize this operational mode for dynamical decoupling experiments to probe the charge noise power spectrum in a silicon metal-oxide-semiconductor double quantum dot. In addition, we assess qubit frequency drift over longer timescales to capture low-frequency noise. We present the charge noise power spectral density up to 3 MHz, which exhibits a 1/fα dependence consistent with α ~ 0.7, over 9 orders of magnitude in noise frequency.

This is the user manual for EMPIRE, a simulation code for electromagnetics and plasma physics.

Neural operators [1–5] have recently become popular tools for designing solution maps between function spaces in the form of neural networks. Differently from classical scientific machine learning approaches that learn parameters of a known partial differential equation (PDE) for a single instance of the input parameters at a fixed resolution, neural operators approximate the solution map of a family of PDEs [6,7]. Despite their success, the uses of neural operators are so far restricted to relatively shallow neural networks and confined to learning hidden governing laws. In this work, we propose a novel nonlocal neural operator, which we refer to as nonlocal kernel network (NKN), that is resolution independent, characterized by deep neural networks, and capable of handling a variety of tasks such as learning governing equations and classifying images. Our NKN stems from the interpretation of the neural network as a discrete nonlocal diffusion reaction equation that, in the limit of infinite layers, is equivalent to a parabolic nonlocal equation, whose stability is analyzed via nonlocal vector calculus. The resemblance with integral forms of neural operators allows NKNs to capture long-range dependencies in the feature space, while the continuous treatment of node-to-node interactions makes NKNs resolution independent. The resemblance with neural ODEs, reinterpreted in a nonlocal sense, and the stable network dynamics between layers allow for generalization of NKN's optimal parameters from shallow to deep networks. This fact enables the use of shallow-to-deep initialization techniques [8]. Our tests show that NKNs outperform baseline methods in both learning governing equations and image classification tasks and generalize well to different resolutions and depths.

Fractional equations have become the model of choice in several applications where heterogeneities at the microstructure result in anomalous diffusive behavior at the macroscale. In this work we introduce a new fractional operator characterized by a doubly-variable fractional order and possibly truncated interactions. Under certain conditions on the model parameters and on the regularity of the fractional order we show that the corresponding Poisson problem is well-posed. We also introduce a finite element discretization and describe an efficient implementation of the finite-element matrix assembly in the case of piecewise constant fractional order. Through several numerical tests, we illustrate the improved descriptive power of this new operator across media interfaces. Furthermore, we present one-dimensional and two-dimensional h-convergence results that show that the variable-order model has the same convergence behavior as the constant-order model.

The recent discovery of bright, room-temperature, single photon emitters in GaN leads to an appealing alternative to diamond best single photon emitters given the widespread use and technological maturity of III-nitrides for optoelectronics (e.g. blue LEDs, lasers) and high-speed, high-power electronics. This discovery opens the door to on-chip and on-demand single photon sources integrated with detectors and electronics. Currently, little is known about the underlying defect structure nor is there a sense of how such an emitter might be controllably created. A detailed understanding of the origin of the SPEs in GaN and a path to deterministically introduce them is required. In this project, we develop new experimental capabilities to then investigate single photon emission from GaN nanowires and both GAN and AlN wafers. We ion implant our wafers with the ion implanted with our focused ion beam nanoimplantation capabilities at Sandia, to go beyond typical broad beam implantation and create single photon emitting defects with nanometer precision. We've created light emitting sources using Li⁺ and He⁺, but single photon emission has yet to be demonstrated. In parallel, we calculate the energy levels of defects and transition metal substitutions in GaN to gain a better understanding of the sources of single photon emission in GaN and AlN. The combined experimental and theoretical capabilities developed throughout this project will enable further investigation into the origins of single photon emission from defects in GaN, AlN, and other wide bandgap semiconductors.

Geologic Disposal Safety Assessment Framework is a state-of-the-art simulation software toolkit for probabilistic post-closure performance assessment of systems for deep geologic disposal of nuclear waste developed by the United States Department of Energy. This paper presents a generic reference case and shows how it is being used to develop and demonstrate performance assessment methods within the Geologic Disposal Safety Assessment Framework that mitigate some of the challenges posed by high uncertainty and limited computational resources. Variance-based global sensitivity analysis is applied to assess the effects of spatial heterogeneity using graph-based summary measures for scalar and time-varying quantities of interest. Behavior of the system with respect to spatial heterogeneity is further investigated using ratios of water fluxes. This analysis shows that spatial heterogeneity is a dominant uncertainty in predictions of repository performance which can be identified in global sensitivity analysis using proxy variables derived from graph descriptions of discrete fracture networks. New quantities of interest defined using water fluxes proved useful for better understanding overall system behavior.

The prevalence of COVID-19 is shaped by behavioral responses to recommendations and warnings. Available information on the disease determines the population’s perception of danger and thus its behavior; this information changes dynamically, and different sources may report conflicting information. We study the feedback between disease, information, and stay-at-home behavior using a hybrid agent-based-system dynamics model that incorporates evolving trust in sources of information. We use this model to investigate how divergent reporting and conflicting information can alter the trajectory of a public health crisis. The model shows that divergent reporting not only alters disease prevalence over time, but also increases polarization of the population’s behaviors and trust in different sources of information.

The long-standing problem of predicting the electronic structure of matter on ultra-large scales (beyond 100,000 atoms) is solved with machine learning.