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DOE OSTI2020

PETSc Users Manual (Rev. 3.13)

This manual describes the use of PETSc for the numerical solution of partial differential equations and related problems on high-performance computers. The Portable, Extensible Toolkit for Scientific Computation (PETSc) is a suite of data structures and routines that provide the building blocks for the implementation of large-scale application codes on parallel (and serial) computers. PETSc uses the MPI standard for all message-passing communication. PETSc includes an expanding suite of parallel linear solvers, nonlinear solvers, and time integrators that may be used in application codes written in Fortran, C, C++, and Python. PETSc provides many of the mechanisms needed within parallel application codes, such as parallel matrix and vector assembly routines. The library is organized hierarchically, enabling users to employ the level of abstraction that is most appropriate for a particular problem. By using techniques of object-oriented programming, PETSc provides enormous flexibility for users. PETSc is a sophisticated set of software tools; as such, for some users it initially has a much steeper learning curve than a simple subroutine library. In particular, for individuals without some computer science background, experience programming in C, C++, python, or Fortran and experience using a debugger such as gdb or dbx, it may require a significant amount of time to take full advantage of the features that enable efficient software use. However, the power of the PETSc design and the algorithms it incorporates may make the efficient implementation of many application codes simpler than \rolling them" yourself.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Development of Microreactor Automated Control System (MACS): Surrogate Plant-level Modeling and Control Algorithms Integration

This report discusses progress on the modeling and integration task as part of the development of Microreactor Automated Control System (MACS). What follows is a discussion of the software tools used to develop a surrogate microreactor plant-level model, MACS module development, and a summary of the findings from integration with a hardware-in-the-loop (HIL) setup at Idaho National Laboratory (INL). Oak Ridge National Laboratory worked with INL to understand available hardware at INL (such as existing control platforms). With this information and using a preliminary framework for MACS with software interfaces defined, surrogate models and initial automated control algorithms were created for integration into the hardware to provide a HIL demonstration platform for MACS. Available reduced order reactor models that leverage existing microreactor neutronics and thermal hydraulics models have been integrated in the surrogate plant-level model. The surrogate model has been evaluated for sensitivity of all parameters and the MACS software modules (including the surrogate model) have been demonstrated to interact with the hardware. The integration, however, pointed to the need for further improvements to the framework—and specifically improvements to the interfaces to ensure that the HIL simulator is capable of longer-term stable operation with MACS in the loop. These improvements will be the focus of future research.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Opportunities for retrieval and tool augmented large language models in scientific facilities

Upgrades to advanced scientific user facilities such as next-generation x-ray light sources, nanoscience centers, and neutron facilities are revolutionizing our understanding of materials across the spectrum of the physical sciences, from life sciences to microelectronics. However, these facility and instrument upgrades come with a significant increase in complexity. Driven by more exacting scientific needs, instruments and experiments become more intricate each year. This increased operational complexity makes it ever more challenging for domain scientists to design experiments that effectively leverage the capabilities of and operate on these advanced instruments. Large language models (LLMs) can perform complex information retrieval, assist in knowledge-intensive tasks across applications, and provide guidance on tool usage. Using x-ray light sources, leadership computing, and nanoscience centers as representative examples, we describe preliminary experiments with a Context-Aware Language Model for Science (CALMS) to assist scientists with instrument operations and complex experimentation. With the ability to retrieve relevant information from facility documentation, CALMS can answer simple questions on scientific capabilities and other operational procedures. With the ability to interface with software tools and experimental hardware, CALMS can conversationally operate scientific instruments. By making information more accessible and acting on user needs, LLMs could expand and diversify scientific facilities’ users and accelerate scientific output.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Methodology and Tool for the Physical Security Analysis of Micro and Advanced Reactors

This work proposes a dynamic evaluation methodology to relax the conservatism in physical security evaluation, by leveraging an ongoing work in the Light Water Reactor Sustainability pathway. This methodology is implemented in a dynamic risk assessment tool named Event Modeling Risk Assessment using Linked Diagrams (EMRALD). The work extends EMRALD’s capability to support a sandbox feature where analysts can easily create attack scenarios and modify advanced/small modular reactor (A/SMR) security and safety features using templates. This approach saves time and cost since the analysis does not require creating detailed computer-aided design models, as is commonly required in commercial force-on-force software tools. EMRALD is completely free to use at https://emraldapp.inl.gov. We have developed basic templates including physical barriers, intrusion sensors, physical areas, and safety actions, that can be downloaded from EMRALD’s GitHub site: https://github.com/idaholab/EMRALD. These templates use generic data commonly used for training purposes, which do not reflect any actual operating nuclear reactor. Users may adjust the data in the templates with their own dataset and/or create new templates in EMRALD. The proposed methodology combines security and safety by assessing sabotage effects up to the radiological consequence to the public instead of merely the core damage state. This practice follows the industry standard for advanced non-light-water reactors currently proposed for endorsement by the Nuclear Regulatory Commission. The combination of security and safety is expressed in an achievability-consequence chart. EMRALD can be used to generate data for this chart. A hypothetical case study using a representative sodium-cooled fast reactor (SFR) facility is presented in this report to demonstrate this methodology. This case study does not contain any actual nuclear plant information. This work will benefit A/SMR vendors and utilities to implement security by design during the reactor design iteration phase, such that they do not have to perform upgrades and retrofits to the reactor after it is installed to improve its physical protection system. The tool may also be used to analyze domestic or foreign reactor designs to support the International Nuclear Security Techniques for Advanced Reactors (INSTAR) bilateral missions. Future works are planned to implement the methodology on a reference SFR reactor and a reference high-temperature gas-cooled reactor to obtain insights and lessons-learned for the A/SMR community.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Bolduc, Benjamin (ORCID:0000000324200755)↗

DOE OSTI2020

CBRN Situational Awareness Tools for the Modern Age

CBRN Situational awareness (SA) should be a key operational requirement in the CNI area of discussion, not only for the “boots-on-the-ground” warfighter, but at a strategic level. For example, maneuver plans will need to be developed for contamination avoidance and battlefield survivability. Large datasets from instruments dispersed across the battlefield will thus need to be collected and processed into a holistic assessment of the radiological hazard. From there, hazard maps then must be distributed at the tactical level, all while continuing to effectively engage a peer adversary. This vision represents a network of sensors, software tools, data processing algorithms, communications suites, and common operational picture (COP) platforms working in concert to inform warfighters and command echelons alike of evolving nuclear and radiological hazards. This complex system-of-systems and the ultimate goal of effective engagement in a nuclear or radiological-hazard battlefield can be achieved through pursuit of improvement in collaborative SA tools.

Becker, Eric M.↗

DOE OSTI2022

BLAST aka: BLAST-Py see also BLAST-Lite (Battery Lifetime Analysis and Simulation Tool Suite - Python) [SWR-22-69]

Battery Lifetime Analysis and Simulation Tool Suite (BLAST or BLAST-Py) developed in the Python programming language. BLAST-Py predicts the evolution of lithium-ion battery performance metrics over their lifetime, using models trained on lab-based accelerated aging data to predict battery performance in dynamic, real-world use. BLAST-Py contains existing models for a variety of lithium-ion battery chemistries (NMC/Gr and LFP/Gr). See also the open-source version of this software tool known as "BLAST-Lite" at: https://github.com/NREL/BLAST-Lite

Smith, Kandler↗

DOE OSTI2024

Light Water Reactor Sustainability Program: Upgrade of EMRALD to a Modern JavaScript-based Framework

Event Modeling Risk Assessment using Linked Diagrams (EMRALD) is a software tool developed at Idaho National Laboratory for researching the capabilities of dynamic probabilistic risk assessment. It provides a simple interface to represent complex interactions often seen when developing dynamic models. EMRALD can also interface with other applications by modifying inputs, running, and using their results within EMRALD for dynamic and integrated assessment. This report goes over the work performed as part of the Risk-Informed Systems Analysis Pathway under the Light Water Reactor Sustainability program to upgrade the EMRALD software.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

DINGO: Digital assistant to grid operators for resilience management of power distribution system

With increasing adverse weather events and disasters, enabling resiliency of the power distribution system (PDS) is becoming increasingly important. Here in this work, resiliency is defined as the systems ability to keep supplying critical loads even with multiple contingencies. Resiliency may depend on: (a) advanced tools to assist operators in situational awareness and decision making with the increasing volume of data generated by the PDS, (b) visualization and ease of interaction with system resources and information, especially during extreme events and resulting human operator stress, and (c) flexible resources and autonomous control. Operators and support engineers need to interact with the system for key information and take action under stress, given the requirement for decisions in a short time. Integrated technological solutions are prevailing steps to support the most appropriate decision during critical times to serve essential loads. In order to meet the required goals, a Real-time Resiliency Monitoring and Operational Decision Support (RT-RMOD) tool have been developed. It supports various functionalities, including real-time monitoring, resilience assessment, and proactive decision support. However, this work makes advanced feature additions to the tool by developing data-enabled resilience management algorithms for (i) outage detection and localization, (ii) Resiliency-metric driven restoration and reconfiguration, and (iii) NLP based digital assistant for operators called DINGO (DIgital assistaNt to Grid Operators) to interact with Advanced Distribution Management System (ADMS) and RT-RMOD. The developed algorithm was validated for multiple cases of weather events using a real-world, off-grid microgrid system modeled in a real-time simulator, sensor data, and software tools.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Tusqh

SAND2025-00675O Tusqh is a software tool that generates cubical meshes in 2D and 3D and computes the homology of these meshes using persistent homology. It includes a grid cell in the output if its volume-fraction is above a selectable threshold, estimated by sampling points within the cell. Tusqh incorporates anti-aliasing algorithms to mitigate grid orientation and scale effects. It is designed for creating finite element meshes for simulations and can be used in various applications such as heat diffusion, mechanical simulations, and computer graphics rendering. The software outputs meshes in an open format compatible with downstream software. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

SciDAC↗

DOE OSTI2026

Generative Models for Crystalline Materials

Understanding structure-property relationships in materials is fundamental in condensed matter physics and materials science. Over the past few years, machine learning (ML) has emerged as a powerful tool for advancing this understanding and accelerating materials discovery. Early ML approaches primarily focused on constructing and screening large material spaces to identify promising candidates for various applications. More recently, research efforts have increasingly shifted toward generating crystal structures using end-to-end generative models. This review analyzes the current state of generative modeling for crystal structure prediction and de novo generation. It examines crystal representations, outlines the generative models used to design crystal structures, and evaluates their respective strengths and limitations. Furthermore, the review highlights experimental considerations for evaluating generated structures and provides recommendations for suitable existing software tools. Emerging topics, such as modeling disorder and defects, integration in advanced characterization, incorporating synthetic feasibility constraints, and model explainability are explored. Ultimately, this work aims to inform both experimental scientists looking to adapt suitable ML models to their specific circumstances and ML specialists seeking to understand the unique challenges related to inverse materials design and discovery.

Metni, Houssam [Karlsruhe Inst. of Technology (KIT↗

DOE OSTI2021

Unified Nanotechnology Format: One Way to Store Them All

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamComboDMLinear

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamComboDMGeometric

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Enabling Low-Temperature (LTP) Ignition Technologies for Multi-Mode Engines through the Development of a Validated High-Fidelity LTP Model for Predicative Simulations Tools

The goal of multi-mode engine architectures is to extend current lean-burn dilution limits with renewable fuels, which requires spark plugs to deposit high energies (hundreds of mJ) in order to initiate ignition and complete combustion. At elevated energy deposition rates, spark plugs experience increased electrode erosion and thermal losses, which ultimately shortens the spark-plug lifetime and lowers ignition efficiency. As such, in order to safeguard the efficiency gains of multi-mode concepts, new and improved ignition technologies are required. Recently, non-equilibrium low-temperature plasmas (LTP) have been shown to promote energy-efficient ignition via quenching and transport of electronically excited atoms and molecules, selective radical production and fast heating of hydrocarbon/air mixtures [1-2]. Thus, LTP is seen as a technology that can potentially improve the energy extraction efficiency of fuels, while enabling kinetically controlled combustion modes towards fuel leaner conditions to realize current DOE VTO goals of improving the sustainability of future mobility [3]. Although many previous studies have demonstrated the efficacy of plasma-assisted ignition to enhance combustion, the detailed enhancement mechanisms remain largely unknown, especially for oxygenated fuels and at elevated pressures that are most relevant to practical engine conditions. These barriers hinder the development of accurate and comprehensive numerical models that seek to describe LTP-based ignition in existing engine design software tools and methods. Current state-of-the-art simulation capabilities for LTP ignition systems are in need of improvements since they deliver qualitative results only due to important limitations of existing approaches. Firstly, validated kinetic models with elementary steps for plasma discharges in oxygenated fuel/air mixtures of relevance to the transportation sector are required. Such kinetic models do not exist at present and will be developed and validated within this project. Secondly, plasma discharges and reactive mixture ignition are multi-scale, unsteady processes requiring high-performance numerical methods and software that execute efficiently on DOE supercomputers. Such software does not exist at present and will be developed and applied to practical LTP ignition scenarios as part of this project. Thirdly, experimental databases that are tailored to serve as benchmark in support of the development of predictive computational models of LTP ignition do not exist and will be part of this project.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2020

Exploiting Colorimetry for Fidelity in Data Visualization

Advances in multimodal characterization methods fuel the generation of increasing immense hyper-dimensional data sets. Color mapping is employed for conveying higher dimensional data in two-dimensional (2D) representations for human consumption without relying on multiple projections. How one constructs these color maps, however, critically affects how accurately one perceives data. For simple scalar fields, perceptually uniform color maps and color selection have been shown to improve data readability and interpretation across research fields. In this work, we review core concepts underlying the design of perceptually uniform color maps and extend the concepts from scalar fields to two-dimensional vector fields and three-component composition fields frequently found in materials-chemistry research to enable high-fidelity visualization. Additionally, we develop the software tools PAPUC and CMPUC to enable researchers to utilize these colorimetry principles and employ perceptually uniform color spaces for rigorously meaningful color mapping of higher dimensional data representations. Last, we demonstrate how these approaches deliver immediate improvements in data readability and interpretation in microscopies and spectroscopies routinely used in discerning materials structure, chemistry, and properties.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Integration of the NCRC Database and Other INL Databases

The Nuclear Computational Resource Center provides a portal by which industry professionals, educational staff, students, national laboratory employees, and others may request access to certain engineering software tools. As the tools provided through the Nuclear Computational Resource Center portal are not open-source and freely available, a set of approvals are necessary before access is granted. All code recipients must be associated with an institution that has a license with Idaho National Laboratory for the code requested. Information about these licenses is controlled by Idaho National Laboratory’s Technology Deployment organization and housed in a Technology Deployment database. Those requesting code access who are not citizens of the United States must also have a security plan, mandated by Idaho National Laboratory policy. Security plans are managed by the International Access Program and are stored in an International Access Program database known as IFacts. Granting access to software thus depends on information stored in the Technology Deployment database and IFacts. In the past, no connection between the Nuclear Computational Resource Center portal and these databases existed, making checking the status of license agreements and security plans time consuming and error prone. This report demonstrates that the Nuclear Computational Resource Center portal now connects to both the Technology Deployment database and IFacts, greatly improving the ease of use of the Nuclear Computational Resource Center system for administrators, which leads to a better overall experience for those requesting code access.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

DLIO: A DATA-CENTRIC BENCHMARK FOR DEEP LEARNING APPLICATIONS

SF-22-136 Deep learning has been shown as a successful method for various tasks, and its popularity results in numerous open-source deep learning software tools. Deep learning has been applied to a broad spectrum of scientific domains such as cosmology, particle physics, computer vision, fusion, and astrophysics. Scientists have performed a great deal of work to optimize the computational performance of deep learning frameworks. However, the same cannot be said for I/O performance. As deep learning algorithms rely on big-data volume and variety to effectively train neural networks accurately, I/O is a significant bottleneck on large-scale distributed deep learning training. DLIO, is a novel representative benchmark suite built based on the I/O profiling of the selected workloads. DLIO can be utilized to accurately emulate the I/O behavior of modern deep learning applications. Using DLIO, application developers and system software solution architects can identify potential I/O bottlenecks in their applications and guide optimizations to boost the I/O performance leading to lower training times. The storage vendor can also use DLIO as a guide for designing and optimize the storage and filesystem targeting at deep learning application.

ZHENG, HUIHUO↗