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DOE OSTI2022

Xyce™ Parallel Electronic Simulator Users' Guide, Version 7.5.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. (2) A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. (3) Device models that are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase — a message passing parallel implementation — which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Xyce™ Parallel Electronic Simulator Users' Guide (V.7.6)

This manual describes the use of the Xyce™ Parallel Electronic Simulator. Xyce™ has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. (2) A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. (3) Device models that are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices. Xyce™ is a parallel code in the most general sense of the phrase—a message passing parallel implementation—which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel eficiency is achieved as the number of processors grows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Xyce™ Parallel Electronic Simulator Users’ Guide, Version 7.8

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. (2) A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. (3) Device models that are specifically tailored to meet Sandia’s needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase — a message passing parallel implementation — which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

42 ENGINEERING↗

DOE OSTI2020

Compare linear-system solver and preconditioner stacks with emphasis on GPU performance and propose phase-2 NGP solver development pathway

The goal of the ExaWind project is to enable predictive simulations of wind farms comprised of many megawatt-scale turbines situated in complex terrain. Predictive simulations will require computational fluid dynamics (CFD) simulations for which the mesh resolves the geometry of the turbines and captures the rotation and large deflections of blades. Whereas such simulations for a single turbine are arguably petascale class, multi-turbine wind farm simulations will require exascale-class resources. The primary physics codes in the ExaWind project are Nalu-Wind, which is an unstructured-grid solver for the acoustically incompressible Navier-Stokes equations, and OpenFAST, which is a whole-turbine simulation code. The Nalu-Wind model consists of the mass-continuity Poisson-type equation for pressure and a momentum equation for the velocity. For such modeling approaches, simulation times are dominated by linear-system setup and solution for the continuity and momentum systems. For the ExaWind challenge problem, the moving meshes greatly affect overall solver costs as reinitialization of matrices and recomputation of preconditioners is required at every time step. In this report we evaluated GPU-performance baselines for the linear solvers in the Trilinos and hypre solver stacks using two representative Nalu-Wind simulations: an atmospheric boundary layer precursor simulation on a structured mesh, and a fixed-wing simulation using unstructured overset meshes. Both strong-scaling and weak-scaling experiments were conducted on the OLCF supercomputer Summit and similar proxy clusters. We focused on the performance of multi-threaded Gauss-Seidel and two-stage Gauss-Seidel that are extensions of classical Gauss-Seidel; of one-reduce GMRES, a communication-reducing variant of the Krylov GMRES; and algebraic multigrid methods that incorporate the afore-mentioned methods. The team has established that AMG methods are capable of solving linear systems arising from the fixed-wing overset meshes on CPU, a critical intermediate result for ExaWind FY20 Q3 and Q4 milestones. For the fixed-wing strong-scaling study (model with 3M grid-points), the team identified that Nalu-Wind simulations with the new Trilinos and hypre solvers scale to modest GPU counts, maintaining above 70% efficiency up to 6 GPUs. However, there still remain significant bottlenecks to performance: matrix assembly (hypre), AMG setup (hypre and Trilinos) In the weak-scaling experiments (going from 0.4M to 211M gridpoints), it's shown that the solver apply phases are faster on GPUs, but that Nalu-Wind simulation times grow, primarily due to the multigrid-setup process. Finally, based on the report outcomes, we propose a linear solver path-forward for the remainder of the ExaWind project. Near term, the NREL team will continue their work on GPU-based linear-system assembly. They will also investigate how the use of alternatives to the NVIDIA UVM (unified virtual memory) paradigm affects performance. Longer term, the NREL team will evaluate algorithmic performance on other types of accelerators and merge their improvements back to the main hypre repository branch. Near term, the Trilinos team will address performance bottlenecks identified in this milestone, such as implementing a GPU-based segregated momentum solve and reusing matrix graphs across linear-system assembly phases. Longer term, the Trilinos team will do detailed analysis and optimization of multigrid setup.

17 WIND ENERGY↗

DOE OSTI2022

LaSDI: Parametric Latent Space Dynamics Identification

Enabling fast and accurate physical simulations with data has become an important area of computational physics to aid in inverse problems, design-optimization, uncertainty quantification, and other various decision-making applications. This paper presents a data-driven framework for parametric latent space dynamics identification procedure that enables fast and accurate simulations. The parametric model is achieved by building a set of local latent space model and designing an interaction among them. An individual local latent space dynamics model achieves accurate solution in a trust region. By letting the set of trust region to cover the whole parameter space, our model shows an increase in accuracy with an increase in training data. Herein we introduce two different types of interaction mechanisms, i.e., point-wise and region-based approach. Both linear and nonlinear data compression techniques are used. We illustrate the framework of Latent Space Dynamics Identification (LaSDI) enable a fast and accurate solution process on various partial differential equations, i.e., Burgers’ equations, radial advection problem, and nonlinear heat conduction problem, achieving 0 (100)x speed-up and 0 (1)% relative error with respect to the corresponding full order models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Prevalence of typical operational problems and energy savings opportunities in U.S. commercial buildings

In the United States, as much as 30% of the 19 EJ that commercial buildings consume is considered excess. Much of the excess energy is due to the inability to manage building operations efficiently. Because almost 20% of the total primary energy consumption is associated with commercial buildings, significant energy reductions in this sector are needed to mitigate climate change. Therefore, many cities and states are mandating periodic “tune-ups” of these buildings to eliminate excess energy consumption. Although the benefits of tune-ups and retro-commissioning are clear, focusing these mandates to look for specific opportunities has been a challenge because of the lack of studies that document the prevalence of opportunities. Therefore, we analyzed building automation system data from 151 buildings across the United States to document common operational problems and opportunities to improve building operations. This analysis showed that opportunities to improve building operations exist in almost every building. These opportunities were not strongly correlated with building vintage or size, but were reflective of how the buildings are operated. The prevalence of the top 20 opportunities ranged between 74% and 23%, with 40% of these associated with air-handling units. The rest of the opportunities are associated with schedules, chilled and hot-water distribution, and zone controls. Of the 151 buildings, 69 of them implemented corrective actions of some or all opportunities that were identified. Implementation varied across the Re-tuning categories, with 60% for schedule opportunities, 50% for zone opportunities, over 40% for the air-handling unit and hot-water opportunities, and 35% of the chilled-water opportunities. There was wide variation in whole building energy savings, ranging from 0 to 50% and 0 to 18 $/m2 with median percent annual whole building savings of 12% and median normalized annual cost savings of $1.75/m2. In addition to documenting these key findings, the paper provides a list of opportunities that can be automatically and continuously identified and corrected and offers a list of those opportunities that should be the focus of the mandates.

Katipamula, Srinivas↗

DOE OSTI2020

Mechanical Regulation of Photosynthesis in Cyanobacteria

Photosynthetic organisms regulate their responses to many diverse stimuli in an effort to balance light harvesting with utilizable light energy for carbon fixation and growth (source–sink regulation). This balance is critical to prevent the formation of reactive oxygen species that can lead to cell death. However, investigating the molecular mechanisms that underlie the regulation of photosynthesis in cyanobacteria using ensemble-based measurements remains a challenge due to population heterogeneity. Here, to address this problem, we used long-term quantitative time-lapse fluorescence microscopy, transmission electron microscopy, mathematical modelling and genetic manipulation to visualize and analyse the growth and subcellular dynamics of individual wild-type and mutant cyanobacterial cells over multiple generations. We reveal that mechanical confinement of actively growing Synechococcus sp. PCC 7002 cells leads to the physical disassociation of phycobilisomes and energetic decoupling from the photosynthetic reaction centres. We suggest that the mechanical regulation of photosynthesis is a critical failsafe that prevents cell expansion when light and nutrients are plentiful, but when space is limiting. These results imply that cyanobacteria must convert a fraction of the available light energy into mechanical energy to overcome frictional forces in the environment, providing insight into the regulation of photosynthesis and how microorganisms navigate their physical environment.

BASIC BIOLOGICAL SCIENCES,BIOMASS FUELS↗

DOE OSTI2024

Modifying the Asynchronous Jacobi Method for Data Corruption Resilience

Moving scientific computation from high-performance computing (HPC) and cloud computing (CC) environments to devices on the edge, i.e., physically near instruments of interest, has received tremendous interest in recent years. Such edge computing environments can operate on data in situ, offering enticing benefits over data aggregation to HPC and CC facilities that include avoiding costs of transmission, increased data privacy, and real-time data analysis. Because of the inherent unreliability of edge computing environments, new fault-tolerant approaches must be developed before the benefits of edge computing can be realized. Motivated by algorithm-based fault tolerance, a variant of the asynchronous Jacobi (ASJ) method is developed that achieves resilience to data corruption by rejecting solution approximations from neighbor devices according to a bound derived from convergence theory. Numerical results on a two-dimensional Poisson problem show that the new rejection criterion, along with a novel approximation to the shortest path length on which the criterion depends, restores convergence for the ASJ variant in the presence of certain types data corruption. Numerical results are obtained for when the singular values in the analytic bound are approximated. Additional linear systems are also explored, one with a more dense sparsity pattern and one that includes advection. All results indicate that successful resilience to data corruption depends on whether the bound tightens fast enough to reject corrupted data before the iteration evolution deviates significantly from that predicted by the convergence theory defining the bound. This observation generalizes to future work on algorithm-based fault tolerance for other asynchronous algorithms, including upcoming approaches that leverage Krylov subspaces.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Evaluating Deception Detection Model Robustness To Linguistic Variation

With the increasing use of automated, machine learning-driven tools and the downstream impact that algorithmic judgements can have, it is critical to develop models that are robust to evolving or manipulated inputs. Evaluating the reliability of multimodal models across linguistic variations to understand model susceptibility to intentional linguistic adversarial attacks as well as natural linguistic variations is essential in this pursuit. We present extensive analysis of model robustness and susceptibility to linguistic variations in the setting of deceptive news detection, a difficult classification task that is an increasingly important problem to solve with the impact of misinformation spread online. We evaluate the effectiveness of incorporating adversarial defense strategies and measure model susceptibility to state-of-the-art adversarial attacks using two types of linguistic attacks — character and word perturbations. We consider two multiclass prediction tasks — a 3-way classification of tweets as trustworthy, propaganda, or disinformation; and a 4-way classification as clickbait, hoax, satire, or conspiracy — and compare the performance of three embeddings that have been state-of-the-art for several NLP tasks — GloVe, ELMo, and BERT — to highlight consistent trends in susceptibility, high confidence misclassifications, and high impact failures. We find that character or mixed ensemble models are the most effective defense mechanisms and that character perturbations are a more effective attack than word perturbations for deception classification.

adversarial evaluation↗

DOE OSTI2024

Understanding parton evolution in matter from renormalization group analysis

We perform a renormalization group (RG) analysis of collinear hadron production in deep inelastic scattering on nuclei. We consider the limit where the parent parton energy E is large, while the medium opacity remains small. We identify the fixed order and leading enhanced medium contributions to the semi-inclusive cross sections and derive RG equations that resum multiple emissions near the endpoints of the splitting functions at first order in opacity. These evolution equations treat the same type of radiation enhancement in matter as the modified Dokshitzer-Gribov-Lipatov-Altarelli-Parisi approach, but differ in the way one regulates the collinear divergences. They provide a unique analytic insight into the problem of resummation and a faster and more efficient path to phenomenology. The new RG evolution framework is applied to study fragmentation in eA reactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Design of Experiments for Dynamic Test Runs in Solvent-Based CO 2 Capture Pilot Plants

Test runs in the pilot plants consume significant resources, and therefore, the learning from test runs should be maximized. Test runs conducted in the pilot plants are often steady state. It takes several hours for reaching steady-state in the pilot plants, and thus, the duration of the test runs needs to be long even for collecting few steady-state data points. On the other hand, a large number of measurements can be collected through dynamic test runs in a short span of time. This paper presents a systematic design of dynamic experiments (DoDEs) for identifiability of model parameters, which is achieved by persistently exciting the inputs signals. A pseudorandom binary sequence (PRBS) is designed as the input signal for DoDE due to its efficiency in obtaining sufficient spectral content. However, due to the long sequence size of the PRBS signal, a Schroeder-phase input signal, which is a multisine signal, is also designed. Tests for both types of signals are run in the Pilot Solvent Test Unit (PSTU) at the National Carbon Capture Center in Wilsonville, Alabama. The transient data are used to solve dynamic data reconciliation and parameter estimation problem. The estimated parameters are found to be not only superior to those estimated from using data collected from hundreds of steady-state test runs in a nonreactive (air–water) system, but the parameters could be estimated by using the dynamic data collected for about 24 h from the pilot plant for the MEA-H 2 O–CO 2 system.

CO2 capture↗

DOE OSTI2020

Demonstration and performance testing of extreme-resolution simulations with static meshes on Summit (CPU & GPU) for a parked-turbine configuration and an actuator-line (mid-fidelity model) wind farm configuration (ECP-Q4 FY2020 Milestone Report)

17 WIND ENERGY↗

DOE OSTI2024

ARPA-E Grid Optimization (GO) Competition Challenge 1

The ARPA-E Grid Optimization (GO) Competition Challenge 1, from 2018 to 2019, focused on the basic Security Constrained AC Optimal Power Flow problem (SCOPF) for a single time period. The Challenge utilized sets of unique datasets generated by the ARPA-E GRID DATA program. Each dataset consisted of a collection of power system network models of different sizes with associated operating scenarios (snapshots in time defining instantaneous power demand, renewable generation, generator and line availability, etc.). The datasets were of two types: Real-Time, which included starting-point information, and Online, which did not. Week-Ahead data is also provided for some cases but was not used in the Competition. Although most datasets were synthetic and generated by GRIDDATA, a few came from industry and were only used in the Final Event. All synthetic Input Data and Team Results for the GO Competition Challenge 1 for the Sandbox, Trial Events 1 to 3, and the Final Event along with problem, format, scoring and rules descriptions are available here. Data for industry scenarios will not be made public. Challenge 1, a minimization problem, required two computational steps. Solver 1 or Code 1 solved the base SCOPF problem under a strict wall clock time limit, as would be the case in industry, and reported the base case operating point as output, which was used to compute the Objective Function value that was used as the scenario score. The feasibility of the solution was provided by the Solver 2 or Code 2, which solves the power flow problem for all contingencies based on the results from Solver 1. This is not normally done in industry, so the time limits were relaxed. In fact, there were no time limits for Trial Event 1. This proved to be a mistake, with some codes running for more than 90 hours, and a time limit of 2 seconds per contingency was imposed for all other events. Entrants were free to use their own Solver 2 or use an open-source version provided by the Competition. Containers, such as Docker, were considered to improve the portability of codes, but none that could reliably support a multi-node parallel computing environment, e.g., MPI, could be found. For more information on the competition and challenge see the "GO Competition Challenge 1 Information" and "GO Competition Challenge 1 Additional Information" resources below.

ACOPF↗

DOE OSTI2021

Benchmarking blockchain-based gene-drug interaction data sharing methods: A case study from the iDASH 2019 secure genome analysis competition blockchain track

Blockchain distributed ledger technology is just starting to be adopted in genomics and healthcare applications. Despite its increased prevalence in biomedical research applications, skepticism regarding the practicality of blockchain technology for real-world problems is still strong and there are few implementations beyond proof-of-concept. We focus on benchmarking blockchain strategies applied to distributed methods for sharing records of gene-drug interactions. We expect this type of sharing will expedite personalized medicine. We generated gene-drug interaction test datasets using the Clinical Pharmacogenetics Implementation Consortium (CPIC) resource. We developed three blockchain-based methods to share patient records on gene-drug interactions: Query Index, Index Everything, and Dual-Scenario Indexing. We achieved a runtime of about 60 s for importing 4,000 gene-drug interaction records from four sites, and about 0.5 s for a data retrieval query. Our results demonstrated that it is feasible to leverage blockchain as a new platform to share data among institutions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

A fast implicit solver for semiconductor models in one space dimension

Several different approaches are proposed for solving fully implicit discretizations of a simplified Boltzmann-Poisson system with a linear relaxation-type collision kernel. This system models the evolution of free electrons in semiconductor devices under a low-density assumption. At each implicit time step, the discretized system is formulated as a fixed-point problem, which can then be solved with a variety of methods. A key algorithmic component in all the approaches considered here is a recently developed sweeping algorithm for Vlasov-Poisson systems. A synthetic acceleration scheme has been implemented to accelerate the convergence of iterative solvers by using the solution to a drift-diffusion equation as a preconditioner. The performance of four iterative solvers and their accelerated variants has been compared on problems modeling semiconductor devices with various electron mean-free-path.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Evaluating Autoxidation Radical Scavengers and Additives to Enhance Aminopolymer Sorbent Stability

Solid amine sorbents have shown promise in the removal of ultradilute CO 2 from the atmosphere. Despite being a promising candidate material type for this application, these sorbents are prone to degradation during long-term exposure to environmental components such as CO 2 , O 2 , and H 2 O, with amine oxidation being a particularly challenging problem. In this study, we investigate the potency of different radical scavengers and additives in mitigating the degradation of a model poly- (ethylenimine) (PEI)/Al 2 O 3 sorbent under direct air capture (DAC)-relevant conditions. The results reveal that a 4,4′-bis(α,α- dimethylbenzyl)diphenylamine (BDDPA)-incorporated PEI/Al 2 O 3 sorbent showed the most resistance toward oxidative degradation at varying exposure times and BDDPA loadings under CO 2 -free air (21% O 2 /balance N 2 ) at 120 °C. Interestingly, under humid (∼43% relative humidity (RH) at 26 °C) and dry 0.04% CO 2 -air, the BDDPA/PEI/Al 2 O 3 sorbent showed enhanced sorbent stability both at 70 and 120 °C after 4.5 h of exposure. Under humid CO 2 -free air, at 120 °C, the antioxidant performance slightly declined (in comparison to the dry CO 2 -free air condition) but displayed a much higher stability than the pristine sorbent. Overall, the ability of BDDPA to inhibit sorbent degradation under dry and humid, CO 2 -free and CO 2 -containing (0.04%) air at intermediate (70 °C) and elevated (120 °C) temperatures is promising in prolonging sorbent stability and underscores the importance of performing accelerated oxidation studies in the presence of all species that are expected to be present in DAC processes to identify suitable stabilization treatments for sorbent materials.

36 MATERIALS SCIENCE↗

DOE OSTI2021

NEXTorch: A Design and Bayesian Optimization Toolkit for Chemical Sciences and Engineering

Automation and optimization of chemical systems require well-informed decisions on what experiments to run to reduce time, materials, and/or computations. Data-driven active learning algorithms have emerged as valuable tools to solve such tasks. Bayesian optimization, a sequential global optimization approach, is a popular active-learning framework. Past studies have demonstrated its efficiency in solving chemistry and engineering problems. Here we introduce NEXTorch, a library in Python/PyTorch, to facilitate laboratory or computational design using Bayesian optimization. NEXTorch offers fast predictive modeling, flexible optimization loops, visualization capabilities, easy interfacing with legacy software, and multiple types of parameters and data type conversions. It provides GPU acceleration, parallelization, and state-of-the-art Bayesian optimization algorithms and supports both automated an d human-in-the-loop optimization. The comprehensive online documentation introduces Bayesian optimization theory and several examples from catalyst synthesis, reaction condition optimization, parameter estimation, and reactor geometry optimization. NEXTorch is open-source and available on GitHub

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Strong stretching theory for pH-responsive polyelectrolyte brushes in large salt concentrations

Here, we develop a theory for describing the thermodynamics, configuration, and electrostatics of strongly-stretched, pH-responsive polyelectrolyte (PE) brushes in the presence of large salt concentrations. The aim of the paper, therefore, is to study the properties of a PE brush in a salt concentration regime (namely, large concentrations of several molars) that has been hitherto unexplored theoretically in the context of PE brushes but can be routinely encountered in molecular scale simulations of the problem. The brushes are modelled using our recently developed augmented Strong Stretching Theory (SST), while the effect of the presence of the large salt concentration is accounted for by including the contributions of three different types of non-Poisson–Boltzmann (non-PB) effects to the free energy description of the PE brush induced electric double layer (EDL). These non-PB effects are ionic non-mean-field ion–ion correlations, solvent polarization, and the finite size effect of the ions and water dipoles. We study the individual influences of these different effects and show that the ion–ion correlations and solvent polarization effect reduce the brush height which consequently enhances the monomer density and leads to an electrostatic potential distribution of the brush induced EDL that has a larger magnitude at near-wall locations and becomes zero at shorter distances from the wall. The finite size effect, on the other hand, increases the brush height and therefore, weakens the monomer density and leads to a smaller near-wall magnitude of the EDL potential that becomes zero at larger distances from the wall. In time, we consider the impact of all the three non-PB effects simultaneously and show that the ion–ion correlations and solvent polarization effect dominate the size effects and dictate the overall brush configuration and the EDL electrostatics. We also point out that the influence of all the three non-PB effects becomes the largest for a larger salt concentration and a smaller bulk pH. Finally, we compare our theoretical predictions with those obtained from our recently developed all-atom MD simulation model and obtain an excellent match.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗