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NMSBA Sustainable Engineering (Final Report)

Nicholson, Bethany L.; Siirola, John D.

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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Evaluating MPI resource usage summary statistics

Parallel Computing

Ferreira, Kurt B.; Levy, Scott

The Message Passing Interface (MPI) remains the dominant programming model for scientific applications running on today's high-performance computing (HPC) systems. This dominance stems from MPI's powerful semantics for inter-process communication that has enabled scientists to write applications for simulating important physical phenomena. MPI does not, however, specify how messages and synchronization should be carried out. Those details are typically dependent on low-level architecture details and the message characteristics of the application. Therefore, analyzing an application's MPI resource usage is critical to tuning MPI's performance on a particular platform. The result of this analysis is typically a discussion of the mean message sizes, queue search lengths and message arrival times for a workload or set of workloads. While a discussion of the arithmetic mean in MPI resource usage might be the most intuitive summary statistic, it is not always the most accurate in terms of representing the underlying data. In this paper, we analyze MPI resource usage for a number of key MPI workloads using an existing MPI trace collector and discrete-event simulator. Our analysis demonstrates that the average, while easy and efficient to calculate, is a useful metric for characterizing latency and bandwidth measurements, but may not be a good representation of application message sizes, match list search depths, or MPI inter-operation times. Additionally, we show that the median and mode are superior choices in many cases. We also observe that the arithmetic mean is not the best representation of central tendency for data that are drawn from distributions that are multi-modal or have heavy tails. The results and analysis of our work provide valuable guidance on how we, as a community, should discuss and analyze MPI resource usage data for scientific applications.

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Developing Uncertainty Quantification Strategies in Electromagnetic Problems Involving Highly Resonant Cavities

Journal of Verification, Validation and Uncertainty Quantification

Campione, Salvatore; Stephens, John A.; Martin, Nevin; Eckert, Aubrey C.; Warne, Larry K.; Huerta, Jose G.; Pfeiffer, Robert A.; Jones, Adam J.

High-quality factor resonant cavities are challenging structures to model in electromagnetics owing to their large sensitivity to minute parameter changes. Therefore, uncertainty quantification (UQ) strategies are pivotal to understanding key parameters affecting the cavity response. We discuss here some of these strategies focusing on shielding effectiveness (SE) properties of a canonical slotted cylindrical cavity that will be used to develop credibility evidence in support of predictions made using computational simulations for this application.

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Discrete modeling of a transformer with ALEGRA

Rodriguez, Angel E.; Niederhaus, John H.; Greenwood, Wesley J.; Clutz, Christopher J.R.

We report progress on a task to model transformers in ALEGRA using the “Transient Magnetics” option. We specifically evaluate limits of the approach resolving individual coil wires. There are practical limits to the number of turns in a coil that can be numerically modeled, but calculated inductance can be scaled to the correct number of turns in a simple way. Our testing essentially confirmed this “turns scaling” hypothesis. We developed a conceptual transformer design, representative of practical designs of interest, and that focused our analysis. That design includes three coils wrapped around a rectangular ferromagnetic core. The secondary and tertiary coils have multiple layers. The tertiary has three layers of 13 turns each; the secondary has five layers of 44 turns; the primary has one layer of 20 turns. We validated the turns scaling of inductance for simple (one-layer) coils in air (no core) by comparison to available independent calculations for simple rectangular coils. These comparisons quantified the errors versus reduced number of turns modeled. For more than 3 turns, the errors are <5%. The magnetic field solver failed to converge (within 5000 iterations) for >10 turns. Including the core introduced some complications. It was necessary to capture the core surfaces in thin grid sheaths to minimize errors in computed magnetic energy. We do not yet have quantitative benchmarks with which to compare, but calculated results are qualitatively reasonable.

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Document Retrieval and Ranking using Similarity Graph Mean Hitting Times

Dunlavy, Daniel D.; Chew, Peter A.

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.

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Quantifying the unknown impact of segmentation uncertainty on image-based simulations

Nature Communications

Krygier, Michael K.; LaBonte, Tyler; Martinez, Carianne M.; Norris, Chance A.; Sharma, Krish; Collins, Lincoln; Mukherjee, Partha P.; Roberts, Scott A.

Image-based simulation, the use of 3D images to calculate physical quantities, relies on image segmentation for geometry creation. However, this process introduces image segmentation uncertainty because different segmentation tools (both manual and machine-learning-based) will each produce a unique and valid segmentation. First, we demonstrate that these variations propagate into the physics simulations, compromising the resulting physics quantities. Second, we propose a general framework for rapidly quantifying segmentation uncertainty. Through the creation and sampling of segmentation uncertainty probability maps, we systematically and objectively create uncertainty distributions of the physics quantities. We show that physics quantity uncertainty distributions can follow a Normal distribution, but, in more complicated physics simulations, the resulting uncertainty distribution can be surprisingly nontrivial. We establish that bounding segmentation uncertainty can fail in these nontrivial situations. While our work does not eliminate segmentation uncertainty, it improves simulation credibility by making visible the previously unrecognized segmentation uncertainty plaguing image-based simulation.

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Performant implementation of the atomic cluster expansion (PACE) and application to copper and silicon

npj Computational Materials

Lysogorskiy, Yury; Oord, Cas v.; Bochkarev, Anton; Menon, Sarath; Rinaldi, Matteo; Hammerschmidt, Thomas; Mrovec, Matous; Thompson, Aidan P.; Csányi, Gábor; Ortner, Christoph; Drautz, Ralf

The atomic cluster expansion is a general polynomial expansion of the atomic energy in multi-atom basis functions. Here we implement the atomic cluster expansion in the performant C++ code PACE that is suitable for use in large-scale atomistic simulations. We briefly review the atomic cluster expansion and give detailed expressions for energies and forces as well as efficient algorithms for their evaluation. We demonstrate that the atomic cluster expansion as implemented in PACE shifts a previously established Pareto front for machine learning interatomic potentials toward faster and more accurate calculations. Moreover, general purpose parameterizations are presented for copper and silicon and evaluated in detail. We show that the Cu and Si potentials significantly improve on the best available potentials for highly accurate large-scale atomistic simulations.

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Revealing quantum effects in highly conductive δ-layer systems

Communications Physics

Mamaluy, Denis M.; Mendez Granado, Juan P.; Gao, Xujiao G.; Misra, Shashank M.

Thin, high-density layers of dopants in semiconductors, known as δ-layer systems, have recently attracted attention as a platform for exploration of the future quantum and classical computing when patterned in plane with atomic precision. However, there are many aspects of the conductive properties of these systems that are still unknown. Here we present an open-system quantum transport treatment to investigate the local density of electron states and the conductive properties of the δ-layer systems. A successful application of this treatment to phosphorous δ-layer in silicon both explains the origin of recently-observed shallow sub-bands and reproduces the sheet resistance values measured by different experimental groups. Further analysis reveals two main quantum-mechanical effects: 1) the existence of spatially distinct layers of free electrons with different average energies; 2) significant dependence of sheet resistance on the δ-layer thickness for a fixed sheet charge density.

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Timely Reporting of Heavy Hitters Using External Memory

ACM Transactions on Database Systems

Singh, Shikha; Pandey, Prashant; Bender, Michael A.; Berry, Jonathan W.; Farach-Colton, Martín; Johnson, Rob; Kroeger, Thomas M.; Phillips, Cynthia A.

Given an input stream S of size N, a φ-heavy hitter is an item that occurs at least φN times in S. The problem of finding heavy-hitters is extensively studied in the database literature.We study a real-time heavy-hitters variant in which an element must be reported shortly after we see its T = φN-th occurrence (and hence it becomes a heavy hitter). We call this the Timely Event Detection (TED) Problem. The TED problem models the needs of many real-world monitoring systems, which demand accurate (i.e., no false negatives) and timely reporting of all events from large, high-speed streams with a low reporting threshold (high sensitivity).Like the classic heavy-hitters problem, solving the TED problem without false-positives requires large space (ω (N) words). Thus in-RAM heavy-hitters algorithms typically sacrifice accuracy (i.e., allow false positives), sensitivity, or timeliness (i.e., use multiple passes).We show how to adapt heavy-hitters algorithms to external memory to solve the TED problem on large high-speed streams while guaranteeing accuracy, sensitivity, and timeliness. Our data structures are limited only by I/O-bandwidth (not latency) and support a tunable tradeoff between reporting delay and I/O overhead. With a small bounded reporting delay, our algorithms incur only a logarithmic I/O overhead.We implement and validate our data structures empirically using the Firehose streaming benchmark. Multi-threaded versions of our structures can scale to process 11M observations per second before becoming CPU bound. In comparison, a naive adaptation of the standard heavy-hitters algorithm to external memory would be limited by the storage device's random I/O throughput, i.e., ≈100K observations per second.

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Data-driven magneto-elastic predictions with scalable classical spin-lattice dynamics

npj Computational Materials

Nikolov, Svetoslav V.; Wood, Mitchell A.; Cangi, Attila; Maillet, Jean B.; Marinica, Mihai C.; Thompson, Aidan P.; Desjarlais, Michael P.; Tranchida, Julien G.

A data-driven framework is presented for building magneto-elastic machine-learning interatomic potentials (ML-IAPs) for large-scale spin-lattice dynamics simulations. The magneto-elastic ML-IAPs are constructed by coupling a collective atomic spin model with an ML-IAP. Together they represent a potential energy surface from which the mechanical forces on the atoms and the precession dynamics of the atomic spins are computed. Both the atomic spin model and the ML-IAP are parametrized on data from first-principles calculations. We demonstrate the efficacy of our data-driven framework across magneto-structural phase transitions by generating a magneto-elastic ML-IAP for α-iron. The combined potential energy surface yields excellent agreement with first-principles magneto-elastic calculations and quantitative predictions of diverse materials properties including bulk modulus, magnetization, and specific heat across the ferromagnetic–paramagnetic phase transition.

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Polarizable Water Potential Derived from a Model Electron Density

Journal of Chemical Theory and Computation

Rackers, Joshua R.; Silva, Roseane R.; Wang, Zhi; Ponder, Jay W.

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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Characterizing Human Performance: Detecting Targets at High False Alarm Rates [Slides]

Speed, Ann S.; Wheeler, Jason W.; Russell, John L.; Oppel, Fred O.; Sanchez, Danielle; Silva, Austin R.; Chavez , Anna C.

Analysts develop a “no threat” bias with high false alarms. If only shown alarms for actual attacks, may never actually see an alarm. We see this in the laboratory, but not often studied in applied environments. (TSA is an exception.) In this work, near-operational paradigms are useful, but difficult to construct well. Pilot testing is critical before engaging time-limited professionals. Experimental control is difficult to balance with operational realism. Grounding near-operational experiments in basic research paradigms has both advantages and disadvantages. Despite shortcomings in our second experiment, we now have a platform for experimental investigations into the human element of physical security systems.

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Results 151–175 of 9,998
Results 151–175 of 9,998