Publications

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This report summarizes the guidance provided to Sustainable Engineering to help them learn about equation-oriented optimization and the Sandia-developed software packages Pyomo and IDAESPSE. This was a short 10-week project (October 2021 – December 2021) and the goal was to help the company learn about the IDAES framework and how it could be used for their future projects. The company submitted an SBIR proposal related to developing a green ammonia process model with IDAES and if that proposal is successful this NMSBA project could lead to future collaboration opportunities.

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We present a novel approach to information retrieval and document analysis based on graph analytic methods. Traditional information retrieval methods use a set of terms to define a query that is applied against a document corpus to identify the documents most related to those terms. In contrast, we define a query as a set of documents of interest and apply the query by computing mean hitting times between this set and all other documents on a document similarity graph abstraction of the semantic relationships between all pairs of documents. We present the steps of our approach along with a simple example application illustrating how this approach can be used to find documents related to two or more documents or topics of interest.

Compared to the classical Lanczos algorithm, the s-step Lanczos variant has the potential to improve performance by asymptotically decreasing the synchronization cost per iteration. However, this comes at a price; despite being mathematically equivalent, the s-step variant may behave quite differently in finite precision, potentially exhibiting greater loss of accuracy and slower convergence relative to the classical algorithm. It has previously been shown that the errors in the s-step version follow the same structure as the errors in the classical algorithm, but are amplified by a factor depending on the square of the condition number of the O(s)-dimensional Krylov bases computed in each outer loop. As the condition number of these s-step bases grows (in some cases very quickly) with s, this limits the s values that can be chosen and thus can limit the attainable performance. In this work, we show that if a select few computations in s-step Lanczos are performed in double the working precision, the error terms then depend only linearly on the conditioning of the s-step bases. This has the potential for drastically improving the numerical behavior of the algorithm with little impact on per-iteration performance. Our numerical experiments demonstrate the improved numerical behavior possible with the mixed precision approach, and also show that this improved behavior extends to mixed precision s-step CG. Here, we present preliminary performance results on NVIDIA V100 GPUs that show that the overhead of extra precision is minimal if one uses precisions implemented in hardware.

A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.

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The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

Graph algorithms enable myriad large-scale applications including cybersecurity, social network analysis, resource allocation, and routing. The scalability of current graph algorithm implementations on conventional computing architectures are hampered by the demise of Moore’s law. We present a theoretical framework for designing and assessing the performance of graph algorithms executing in networks of spiking artificial neurons. Although spiking neural networks (SNNs) are capable of general-purpose computation, few algorithmic results with rigorous asymptotic performance analysis are known. SNNs are exceptionally well-motivated practically, as neuromorphic computing systems with 100 million spiking neurons are available, and systems with a billion neurons are anticipated in the next few years. Beyond massive parallelism and scalability, neuromorphic computing systems offer energy consumption orders of magnitude lower than conventional high-performance computing systems. We employ our framework to design and analyze new spiking algorithms for shortest path and dynamic programming problems. Our neuromorphic algorithms are message-passing algorithms relying critically on data movement for computation. For fair and rigorous comparison with conventional algorithms and architectures, which is challenging but paramount, we develop new models of data-movement in conventional computing architectures. This allows us to prove polynomial-factor advantages, even when we assume a SNN consisting of a simple grid-like network of neurons. To the best of our knowledge, this is one of the first examples of a rigorous asymptotic computational advantage for neuromorphic computing.

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Reverse engineering (RE) analysts struggle to address critical questions about the safety of binary code accurately and promptly, and their supporting program analysis tools are simply wrong sometimes. The analysis tools have to approximate in order to provide any information at all, but this means that they introduce uncertainty into their results. And those uncertainties chain from analysis to analysis. We hypothesize that exposing sources, impacts, and control of uncertainty to human binary analysts will allow the analysts to approach their hardest problems with high-powered analytic techniques that they know when to trust. Combining expertise in binary analysis algorithms, human cognition, uncertainty quantification, verification and validation, and visualization, we pursue research that should benefit binary software analysis efforts across the board. We find a strong analogy between RE and exploratory data analysis (EDA); we begin to characterize sources and types of uncertainty found in practice in RE (both in the process and in supporting analyses); we explore a domain-specific focus on uncertainty in pointer analysis, showing that more precise models do help analysts answer small information flow questions faster and more accurately; and we test a general population with domain-general sudoku problems, showing that adding "knobs" to an analysis does not significantly slow down performance. This document describes our explorations in uncertainty in binary analysis.

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The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

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The TChem open-source software is a toolkit for computing thermodynamic properties, source term, and source term’s Jacobian matrix for chemical kinetic models that involve gas and surface reactions.

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The peridynamic theory of solid mechanics is applied to modeling the deformation and fracture of micrometer-sized particles made of organic crystalline material. A new peridynamic material model is proposed to reproduce the elastic–plastic response, creep, and fracture that are observed in experiments. The model is implemented in a three-dimensional, meshless Lagrangian simulation code. In the small deformation, elastic regime, the model agrees well with classical Hertzian contact analysis for a sphere compressed between rigid plates. Under higher load, material and geometrical nonlinearity is predicted, leading to fracture. The material parameters for the energetic material CL-20 are evaluated from nanoindentation test data on the cyclic compression and failure of micrometer-sized grains.

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Atomically precise ultradoping of silicon is possible with atomic resists, area-selective surface chemistry, and a limited set of hydride and halide precursor molecules, in a process known as atomic precision advanced manufacturing (APAM). It is desirable to expand this set of precursors to include dopants with organic functional groups and here we consider aluminium alkyls, to expand the applicability of APAM. We explore the impurity content and selectivity that results from using trimethyl aluminium and triethyl aluminium precursors on Si(001) to ultradope with aluminium through a hydrogen mask. Comparison of the methylated and ethylated precursors helps us understand the impact of hydrocarbon ligand selection on incorporation surface chemistry. Combining scanning tunneling microscopy and density functional theory calculations, we assess the limitations of both classes of precursor and extract general principles relevant to each.

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CSPlib is an open source software library for analyzing general ordinary differential equation (ODE) systems and detailed chemical kinetic ODE/DAE systems. It relies on the computational singular perturbation (CSP) method for the analysis of these systems.

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The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

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