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At least 955 records · Page 53

Implementing a unified solver for nonlinearly constrained optimization

SQP and interior-point methods (also referred to as Lagrange-Newton methods) typically share key algorithmic components, such as strategies for computing descent directions and mechanisms that promote global convergence. Building on this insight, we introduce a unifying framework with eight building blocks that abstracts the workflows of Lagrange-Newton methods. We then present Uno, a modular C++ solver that implements our unifying framework and allows the automatic combination of a wide range of strategies with no programming effort from the user. Uno is meant to (1) organize mathematical optimization strategies into a coherent hierarchy; (2) offer a wide range of efficient and robust methods that can be compared for a given instance; (3) enable researchers to experiment with novel optimization strategies; and (4) reduce the cost of development and maintenance of multiple optimization solvers. Uno’s software design allows user to compose new customized solvers for emerging optimization areas such as robust optimization or optimization problems with complementarity constraints, while building on reliable nonlinear optimization techniques. We demonstrate that Uno is highly competitive against state-of-the-art solvers filterSQP, IPOPT, SNOPT, MINOS, LANCELOT, LOQO, and CONOPT on a subset of 429 small problems from the CUTE collection. Uno is available as open-source software under the MIT license at https://github.com/cvanaret/Uno and via its C, Julia, Python, Fortran, and AMPL interfaces.

97 MATHEMATICS AND COMPUTING↗

Techno-Economic Case Study: Low-Temperature Conversion Performance Based on Isolated Anatomical Fractions of Corn Stover

This report summarizes analysis conducted to support a case study under the Feedstock Conversion Interface Consortium (FCIC) focused on techno-economic analysis (TEA) modeling to quantify the process yield and resulting process cost impacts for processing isolated anatomical fractions of corn stover through a low-temperature conversion (biochemical) pathway. It is hypothesized that different individual anatomical fractions of corn stover vary in both composition and recalcitrance, giving biorefineries options in whether and how to deal with fractionated or whole biomass feedstock. By quantifying the techno-economic impacts of this variability, we provide actionable information for end users to understand tradeoffs in conversion system yields and economics in considering feedstock processing decisions at the biorefinery gate. For this study, we worked with FCIC researchers to obtain data on the compositional analysis and conversion performance of whole corn stover alongside three individual anatomical fractions (cobs, husks, and stalks) across key steps of the biorefinery conversion process within FCIC’s research scope—pretreatment and enzymatic hydrolysis. This TEA screening assessment highlighted biorefinery economic trade-offs observed through this approach. Namely, relative to processing whole stover biomass, two of the three anatomical fractions for which composition/conversion data were available (cobs and husks) demonstrated the ability to achieve higher fuel yields and lower minimum fuel selling prices (MFSPs), while the third fraction (stalks) led to the opposite result, as a composite reflection of compositional differences and process convertibility.

cost impacts↗

Data, figures, animations, and scripts associated with the manuscript "Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Carbon Cycling at the Coastal Terrestrial Aquatic Interface"

This package contains the data, figures, animations, and scripts used in "Integrated Effects of Site Hydrology and Vegetation on Exchange Fluxes and Carbon Cycling at the Coastal Terrestrial Aquatic Interface" (Li et al., 2023). This study examines the interactions between soil, vegetation and hydrologic conditions in coastal areas, with a focus on the Chesapeake Bay region. The researchers used a mechanistic model called ATS-PFLOTRAN to explore how these interactions affect exchange process in different regions and the carbon/nitrogen cycle across the terrestrial-aquatic interface (TAI). Simulation scenarios isolate the effects of control factors and reaction constants derived from laboratory experiments. The results show a carbon cycle "hot zone" in coastal wetlands and in the transition zone between wetlands and uplands. Transpiration enhances fluxes between the surface and subsurface domains and increases dissolved oxygen in TAI. The decomposition of leaf-derived organic carbon provides an additional source of carbon for aerobic respiration and denitrification in the TAI. Microbial activity plays a key role in controlling redox conditions and their variability. This modeling study improves the understanding of complex TAI interactions and facilitates the representation of coastal ecosystems in larger-scale Earth system models.Several files can be found from this data package.1. Readme,md: This file describe the Title, Target Journal, Target submission date, Co-author, Science Questions, Hypotheses, Key words, Key message, Model and Data, Repo Structure. The user can read this file first and then go to details.2. mesh.zip: This file contains the mesh file for simulation cases. 3. Figure.zip: This file contains figures used in the manuscript . 4. animation.zip: This file contains animations used in the manuscript . 5. Data.zip: This file contains all required input data, such as concentration and flow boundaries. Also, it contains the DEM and processes results on area fraction. 6. Simulation_setup_and_results.zip: This file contains setup of cases used in the manuscript . The result files are too large, if you need that data, please contact to the Author. 7. notebooks.zip: This file contains the Jupyter notebooks for performing sensitivity analysis and other pre-process and post-process analyses.

54 ENVIRONMENTAL SCIENCES↗

Finite Element Modeling of the Phase Change in Thermally-Grown SiO 2 in SiC Systems for Gas Turbines

The operating lifetimes of SiC-based components in combustion environments are directly linked to the adhesion of the protective environmental barrier coating (EBC) layer. One of the major known failure modes for EBCs is the formation of a thick SiO 2 thermally grown oxide (TGO), which decreases coating adhesion and encourages eventual coating spallation. The effect of the TGO thickness under Yb 2 Si 2 O 7 EBCs on silicon carbide was investigated using finite element models (FEMs) with various interfacial architectures and SiO 2 TGO thicknesses. Further, the FEMs incorporated a user-defined material to simulate the volume contraction of the TGO during the silica phase transformation from β-cristobalite to α-cristobalite upon cooling from the stress-free state at 1350°C to room temperature. Systems with and without a silicon bond coating intermediary layer were assessed. It was shown that the TGO phase transformation stress (1.6–1.7 GPa) dominated the increase in stress in the TGO and EBC layers. Furthermore, it was found that stress increase in the TGO was independent of TGO thickness and interface geometry. These results indicate that stabilization of the TGO to mitigate the phase transformation could dramatically improve the performance of SiC-base components with EBCs.

36 MATERIALS SCIENCE↗

Securing Vehicle Charging Infrastructure

As the US electrifies the transportation sector, cyber attacks targeting vehicle charging could bring consequences to electrical system infrastructure. This is a growing area of concern as charging stations increase power delivery and must communicate to a range of entities to authorize charging, sequence the charging process, and manage load (grid operators, vehicles, OEM vendors, charging network operators, etc.). The research challenges are numerous and are complicated because there are many end users, stakeholders, and software and equipment vendors interests involved. Poorly implemented electric vehicle supply equipment (EVSE), electric vehicle (EV), or grid communication system cybersecurity could be a significant risk to EV adoption because the political, social, and financial impact of cyberattacks - or public perception of such - ripples across the industry and has lasting and devastating effects. Unfortunately, there is no comprehensive EVSE cybersecurity approach and limited best practices have been adopted by the EV/EVSE industry. There is an incomplete industry understanding of the attack surface, interconnected assets, and unsecured interfaces. Thus, comprehensive cybersecurity recommendations founded on sound research are necessary to secure EV charging infrastructure. This project is providing the power, security, and automotive industry with a strong technical basis for securing this infrastructure by developing threat models, determining technology gaps, and identifying or developing effective countermeasures. Specifically, the team is creating a cybersecurity threat model and performing a technical risk assessment of EVSE assets, so that automotive, charging, and utility stakeholders can better protect customers, vehicles, and power systems in the face of new cyber threats.

33 ADVANCED PROPULSION SYSTEMS↗

Caffeine: CoArray Fortran Framework of Efficient Interfaces to Network Environments

This paper provides an introduction to the CoArray Fortran Framework of Efficient Interfaces to Network Environments (Caffeine), a parallel runtime library built atop the GASNet-EX exascale networking library. Caffeine leverages several non-parallel Fortran features to write type- and rank-agnostic interfaces and corresponding procedure definitions that support parallel Fortran 2018 features, including communication, collective operations, and related services. One major goal is to develop a runtime library that can eventually be considered for adoption by LLVM Flang, enabling that compiler to support the parallel features of Fortran. The paper describes the motivations behind Caffeine's design and implementation decisions, details the current state of Caffeine's development, and previews future work. We explain how the design and implementation offer benefits related to software sustainability by lowering the barrier to user contributions, reducing complexity through the use of Fortran 2018 C-interoperability features, and high performance through the use of a lightweight communication substrate.

Rouson, Damian↗

Web-Based Tools for Data-Informed Remedy Optimization: Software Theory and User Guide

This report documents the development and application of two web-based decision-support tools for pump-and-treat (P&T) groundwater remediation systems: PTOLEMY (Pump-and-Treat Optimized Location Evaluation to Maximize Yields) and OPTIMA (Optimization for Pump-and-Treat Implementation, Management, & Assessment). These tools enhance remedy design and management by leveraging advanced computational methods – specifically deep learning and multi-objective optimization – within a user-friendly platform. By integrating data-driven models with established hydrogeological knowledge, PTOLEMY and OPTIMA enable more efficient evaluation of well placement and operational strategies, helping site managers balance multiple remediation objectives under complex conditions. Both tools are implemented as modules within the SOCRATES (Suite Of Comprehensive Rapid Analysis Tools for Environmental Sites) web platform, which provides data access, visualization, and analytics to support remedy optimization across sites in the U.S. Department of Energy Office of Environmental Management complex. PTOLEMY is a rapid screening module designed to identify promising locations for new extraction wells. It employs a multi-channel three-dimensional convolutional neural network (MC3D-CNN) trained on high-fidelity simulation data to predict the relative performance (in terms of contaminant mass recovery) of potential well sites. Through an interactive web interface, PTOLEMY visualizes the probability of high performance across a site, highlighting areas where an extraction well is likely to yield above-threshold contaminant removal over a multi-year period. PTOLEMY’s map-based displays and exportable results support transparent communication of screening analyses. By focusing attention on the most favorable candidate locations, the tool augments traditional engineering judgment and physics-based modeling, providing a data informed basis for subsequent detailed evaluations. OPTIMA is a multi objective optimization module designed to find wellfield layouts and operating schedules that meet various cleanup goals. It quickly evaluates thousands of candidate setups – combinations of well locations, timing, and rates – and returns a small set of best trade-off options for comparison. At its core, OPTIMA uses a U-Net-based surrogate model – a deep-learning emulator of a groundwater flow and transport simulator – to dramatically accelerate scenario evaluations. Coupling this fast surrogate with the NSGA-II (Non-dominated Sorting Genetic Algorithm II) evolutionary algorithm, OPTIMA explores a wide decision space of well locations and schedules to identify Pareto-optimal solutions that trade off key objectives (e.g., minimizing cleanup time, maximizing contaminant mass removal, and minimizing plume extent). The tool outputs a family of optimal configurations and visualizes their trade-offs (Pareto frontiers of cleanup metrics and maps of optimized well placements). Site managers can use these results to understand the range of viable strategies and to select candidate designs for more detailed verification. OPTIMA is currently under active development and not yet fully released; this guide provides early documentation to support planning and gather user feedback.

54 ENVIRONMENTAL SCIENCES↗

Energy Systems Integration Facility (ESIF): World-Class Systems Integration Capabilities and Research

The Energy Systems Integration Facility (ESIF), located at the National Renewable Energy Laboratory (NREL) South Table Mountain campus, is a world-renowned user facility for research and development of modern, advanced, and clean energy technologies. ESIF is distinguished by its continuously evolving, highly integrated systems that span throughout the building, connecting research capabilities across multiple laboratories and test areas. The primary ESIF research systems include: [1] data, cyber, and control networks, [2] research electrical distribution buses (REDB), [3] thermal integration infrastructure, and [4] hydrogen systems. The data, cyber, and control networks provide monitoring, control, communication, automation, visualization, and time series data storage and tagging capabilities for research projects and ESIF systems, including facility safety functions. The REDB system consists of four dedicated AC and DC electrical power networks that can connect devices located across the facility through versatile, automatic circuit configuration to support complex power electronics experiments up to the megawatt-scale. The thermal integration infrastructure consists of three temperature-conditioned water loops that provide heating and cooling interfaces and capabilities for thermal energy research. The hydrogen systems provide megawatt-scale hydrogen production, drying, compression, high-pressure storage, and delivery to laboratory end uses, including hydrogen fuel cell vehicle fueling. The ESIF research systems interconnect and extend throughout the various lab areas of the facility to create elaborate networks composed of diverse technologies for cutting-edge research. The ESIF capabilities are operated and stewarded by the ESIF Research Operations group, who also actively upgrade and advance the systems to ensure they remain ahead of anticipated research - enabling the success of many pioneering energy integration projects. The poster, created by members of the ESIF Research Operations team, highlights and summarizes the four core integrated systems at ESIF. The poster was first presented at the internal NREL Energize Forum on May 13th, 2024, and received the "Best Poster" award.

capabilities↗

A new database website for nuclear level densities

We introduce a new open-access, web-based database (http://nld.ascsn.net), Current Archive of Nuclear Density of Levels (CANDL), that hosts experimental nuclear level density (NLD) datasets from a variety of techniques and energy ranges. Built using the Dash framework in Python, the database is designed to be interactive and user-friendly, allowing researchers to search, visualize, fit, and export NLD data with minimal effort. This resource includes data extracted from evaporation spectra, Oslo method variants, and other experimental techniques that cover excitation energies beyond the neutron resonance region. The database supports on-the-fly fitting with two widely-used phenomenological models—the Constant Temperature (CT) model and the Back-Shifted Fermi Gas (BSFG) model—selected for their simplicity and computational efficiency. Future versions aim to include additional datasets and model types, as well as easy-to-use interfaces to data science techniques. Here, this platform offers a vital tool for the nuclear physics, astrophysics, medicine, and reactor design communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

ERF: Energy Research and Forecasting Model

High performance computing (HPC) architectures have undergone rapid development in recent years. As a result, established software suites face an ever increasing challenge to remain performant on and portable across modern systems. Many of the widely adopted atmospheric modeling codes cannot fully (or in some cases, at all) leverage the acceleration provided by General-Purpose Graphics Processing Units, leaving users of those codes constrained to increasingly limited HPC resources. Energy Research and Forecasting (ERF) is a regional atmospheric modeling code that leverages the latest HPC architectures, whether composed of only Central Processing Units (CPUs) or incorporating GPUs. ERF contains many of the standard discretizations and basic features needed to model general atmospheric dynamics. The modular design of ERF provides a flexible platform for exploring different physics parameterizations and numerical strategies. ERF is built on a state-of-the-art, well-supported, software framework (AMReX) that provides a performance portable interface and ensures ERF's long-term sustainability on next generation computing systems. This paper details the numerical methodology of ERF, presents results for a series of verification/validation cases, and documents ERF's performance on current HPC systems. The roughly 5× speed up of ERF (using GPUs) over Weather Research and Forecasting (CPUs only) for a 3D squall line test case highlights the significance of leveraging GPU acceleration.

17 WIND ENERGY↗

Web of Registries Search (WoRS) v1.0.0

The Web of Registries Search (WoRs) is a web based software application that enables users to search for publicly available biological parts using keywords or sequence fragments. For the initial version (1.0.0) of the application, WoRS targets 10 sources of biological part data: the GenBank NIH genetic sequence database (https://www.ncbi.nlm.nih.gov/genbank/), the iGem parts registry (parts.igem.org), the Addgene plasmid repository (https://www.addgene.org/), and 7 Inventory of Composable Elements (ACS Synbio, JGI, JBEI, JBEI Public, ABF, SynBerc, ABF Public) registry instances. WoRs has built-in automated web scrapers which extract data from sources that do not have a public or well-defined application programming interface (API). They extract as much public data as they can find and create a searchable index to speed up searches. Included in the indexed information is the source of the information.

Plahar, Hector↗

Ad Hoc File Systems for High-Performance Computing

Storage backends of parallel compute clusters are still based mostly on magnetic disks, while newer and faster storage technologies such as flash-based SSDs or non-volatile random access memory (NVRAM) are deployed within compute nodes. Including these new storage technologies into scientific workflows is unfortunately today a mostly manual task, and most scientists therefore do not take advantage of the faster storage media. One approach to systematically include nodelocal SSDs or NVRAMs into scientific workflows is to deploy ad hoc file systems over a set of compute nodes, which serve as temporary storage systems for single applications or longer-running campaigns. This paper presents results from the Dagstuhl Seminar 17202 “Challenges and Opportunities of User-Level File Systems for HPC” and discusses application scenarios as well as design strategies for ad hoc file systems using node-local storage media. The discussion includes open research questions, such as how to couple ad hoc file systems with the batch scheduling environment and how to schedule stage-in and stage-out processes of data between the storage backend and the ad hoc file systems. Also presented are strategies to build ad hoc file systems by using reusable components for networking and how to improve storage device compatibility. Various interfaces and semantics are presented, for example those used by the three ad hoc file systems BeeOND, GekkoFS, and BurstFS. Their presentation covers a range from file systems running in production to cutting-edge research focusing on reaching the performance limits of the underlying devices.

97 MATHEMATICS AND COMPUTING↗

Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.

60 APPLIED LIFE SCIENCES↗

BioSiting Tool (BioSiting) v2

The BioSiting Tool provides a geospatial interface for analyzing bioeconomy resources and infrastructure across the continental U.S. The tool integrates empirical and modeled data from a broad range of sources. Bioeconomy resources mapped in the tool include agricultural residues, forest residues, municipal solid waste streams, food waste, manure, fats, oils and greases and potential yields of energy crops. Infrastructure mapped in the tool includes biorefineries, material recovery facilities, anaerobic digesters, wastewater treatment plants, combustion plants, district energy systems, crude oil pipelines, petroleum pipelines, natural gas pipelines, railways and freight terminals. Additional data layers include environmental justice indicators at the census tract level and carbon dioxide geologic storage potential. Users can select a location on the map, define a buffer radius in kilometers and generate an inventory of all bioecomony resources within the buffer zone. Data from the tool can be downloaded from individual buffer zones, or at the state or national level.

Huntington, Tyler↗

The Viskores User's Guide (V.1.0)

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created Viskores: the visualization toolkit for multi-/many-core architectures. Viskores supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. Viskores also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although Viskores provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.

97 MATHEMATICS AND COMPUTING↗

The Viskores User's Guide, Release 1.1

High-performance computing relies on ever finer threading. Advances in processor technology include ever greater numbers of cores, hyperthreading, accelerators with integrated blocks of cores, and special vectorized instructions, all of which require more software parallelism to achieve peak performance. Traditional visualization solutions cannot support this extreme level of concurrency. Extreme scale systems require a new programming model and a fundamental change in how we design algorithms. To address these issues we created Viskores: the visualization toolkit for multi/many-core architectures. Viskores supports a number of algorithms and the ability to design further algorithms through a top-down design with an emphasis on extreme parallelism. Viskores also provides support for finding and building links across topologies, making it possible to perform operations that determine manifold surfaces, interpolate generated values, and find adjacencies. Although Viskores provides a simplified high-level interface for programming, its template-based code removes the overhead of abstraction.

97 MATHEMATICS AND COMPUTING↗

REopt Lite Overview & Training Exercise

This training exercise provides users with an introduction to and hands-on, interactive exploration of REopt Lite's capabilities. REopt Lite is a free, publicly available techno-economic optimization web tool for distributed energy systems, developed at the National Renewable Energy Laboratory (NREL). REopt Lite helps organizations evaluate the economic viability of grid-connected solar photovoltaics (PV), wind turbines, and battery storage; identify system sizes and battery dispatch strategies to minimize energy costs; and estimate how long a system can sustain critical load during a grid outage. The model is formulated as a mixed-integer linear program based in an underlying application programming interface (API) that is also free and publicly available. This training activity is structured as a group exercise. Participants split into eight groups and each group is assigned a different hypothetical site to model and assess the opportunity for solar PV + battery storage. Groups work together to develop results for their site and then re-convene to compare and discuss results, inputs/drivers of the analysis, and other factors impacting the decision-making process for behind-the-meter solar PV and battery storage.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

MOSCATO Development and Integration in Fiscal Year 2023

In FY23, significant developments were made to the MOSCATO code package, enhancing its capabilities in many aspects. The improvements and advancements can be summarized as follows: Code Restructuring: The MOSCATO code underwent a restructuring process, enabling both Nek5000 and NekRS to share the same interface when using MOSCATO. This integration facilitates smoother interactions between the different modules and streamlines the overall simulation process. Automatic Domain Extension: To allow simulations to propagate over longer time frames, an automatic domain extension capability was added to the metal diffusion module. This enhancement enables more accurate and reliable simulations of diffusion processes, especially in scenarios with extended time requirements. Expanded Corrosion Reactions: The updated MOSCATO package now includes additional reactions that contribute to corrosion. This addition enhances the code’s ability to model corrosion effects more comprehensively, providing a more realistic representation of the systems being studied. Example Case Setup: To assist users and showcase MOSCATO’s capabilities, we developed example cases for various applications. Notably, we created example cases for thermal cells and corrosion loops. These pre-configured cases allow users to get started quickly and effectively with their simulations.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗