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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Science of Scientific Software Development and Use

Increasingly powerful and affordable computing has revolutionized scientific and scholarly discovery across a broad range of fields. Computing relies on software, which has been rapidly growing in scope, diversity, and complexity. At the same time, the methods, processes, and tools used to produce and utilize this essential software are often ad hoc, and the study and improvement of them is often done without the benefit of direct funding or prioritization. Consequently, concerns are growing about the productivity of the developers and users of scientific software, its sustainability, and the trustworthiness of the results that it produces. The US Department of Energy Office of Science (DOE-SC) is at the forefront of modern software-enabled scientific discovery across numerous areas of computational, experimental, and observational science, including major investments in national user facilities that support these activities. In December 2021, the DOE-SC Office of Advanced Scientific Computing Research (ASCR) convened a workshop on basic research needs for the Science of Scientific Software Development and Use (SSSDU). Through keynote presentations, lightning talks, and breakout groups, participants discussed the current practice of software development, maintenance, evolution, and use, and considered how the scientific method could be used to examine these practices and develop more evidence-based approaches to enhance the impact of software and computing on all areas of science. Workshop participants identified three priority research directions (PRDs) and three important crosscutting themes that center on the following overarching insight: software has become an essential part of modern science that impacts new discovery, policy, and technological development. To have full confidence in science delivered via software, we must improve the processes and tools that help us create and use it, and this enhancement requires a deep understanding of the diverse array of teams and individuals doing the work. The full workshop report will be available at https://doi.org/10.2172/1846009.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Modeling and Simulation of Fuel Burnup in Pebble Bed Reactors

Modeling and simulation of fuel burnup plays important roles in reactor design, operation, safety, and security as well as nuclear material control and accounting (MC&A) [1]. This task is uniquely challenging for pebble bed reactors (PBR) because the pebbles are continuously added and recycled into the reactor core, and their paths through the core are random. To address this problem, we present two simulation models in this paper. Brookhaven National Laboratory (BNL) developed a simple lattice model of a PBR in Serpent software to generate used pebble isotopic concentrations. The benefit of using Serpent software in this specific application is that it helps streamline the data generation process without having to use too many independent software codes in combination to achieve a simple task. For example, transport, burnup and zero power decay can be implemented in a single pass. Three-dimensional core models were developed using Serpent to simulate the burnup process of 5 subject pebbles starting from fresh till they reach nearly target burnup, with each pebble placed in one of the five artificially designated radial channels to capture the changing neutron spectra along the core radius. Equilibrium isotopic concentrations were assumed in all other pebbles in the core. To provide a verification for the Serpent isotope transmutation and decay results, Oak Ridge National Laboratory (ORNL) performed simple SCALE/ORIGEN calculations using the average neutron spectra calculated by Serpent for each of the 5 pebbles. The 252-group neutron spectra from Serpent were then used by ORIGEN to produce the one-group library for depletion and decay calculations. The isotopic concentrations of a few nuclides of interest and neutron and gamma source terms produced from the ORIGEN calculations were compared with the ones from the Serpent calculations. The model simulated in this work was based on the Pebble Bed Modular Reactor (PBMR)-400 design because many data needed for the simulation such as core power profiles, fuel and reflector temperatures, and equilibrium core composition are publicly available. In this paper, we will compare the results between these two approaches and benchmark the results against a set of well-established simulation results for PBMR-400.

Dim, Odera↗
DOE OSTI2023

Modeling and Simulation of Fuel Burnup in Pebble Bed Reactors

Modeling and simulation of fuel burnup plays important roles in reactor design, operation, safety, and security as well as nuclear material control and accounting (MC&A) [1]. This task is uniquely challenging for pebble bed reactors (PBR) because the pebbles are continuously added and recycled into the reactor core, and their paths through the core are random. To address this problem, we present two simulation models in this paper. Brookhaven National Laboratory (BNL) developed a simple lattice model of a PBR in Serpent software to generate used pebble isotopic concentrations. The benefit of using Serpent software in this specific application is that it helps streamline the data generation process without having to use too many independent software codes in combination to achieve a simple task. For example, transport, burnup and zero power decay can be implemented in a single pass. Three-dimensional core models were developed using Serpent to simulate the burnup process of five subject pebbles starting from fresh till they reach nearly target burnup, with each pebble placed in one of the five artificially designated radial channels to capture the changing neutron spectra along the core radius. Equilibrium isotopic concentrations were assumed in all other pebbles in the core. To provide a verification for the Serpent isotope transmutation and decay results, Oak Ridge National Laboratory (ORNL) performed simple SCALE/ORIGEN calculations using the average neutron spectra calculated by Serpent for each of the five pebbles. The 252-group neutron spectra from Serpent were then used by ORIGEN to produce the one-group library for depletion and decay calculations. The isotopic concentrations of a few nuclides of interest and neutron and gamma source terms produced from the ORIGEN calculations were compared with the ones from the Serpent calculations. The model simulated in this work was based on the Pebble Bed Modular Reactor (PBMR)-400 design because many data needed for the simulation such as core power profiles, fuel and reflector temperatures, and equilibrium core composition are publicly available. In this paper, we will compare the results between these two approaches and benchmark the results against a set of well-established simulation results for PBMR-400.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2020

Programmable Quantum Networked Microgrids

Quantum key distribution (QKD) provides a potent solution to securely distribute keys for two parties. However, QKD itself is vulnerable to denial of service (DoS) attacks. A flexible and resilient QKD-enabled networked microgrids (NMs) architecture is needed but does not yet exist. In this article, we present a programmable quantum NMs (PQNMs) architecture. It is a novel framework that integrates both QKD and software-defined networking (SDN) techniques capable of enabling scalable, programmable, quantum-engineered, and ultra-resilient NMs. Equipped with a software-defined adaptive post-processing approach, a two-level key pool sharing strategy and an SDN-enabled event-triggered communication scheme, these PQNMs mitigate the impact of DoS attacks through programmable post-processing and secure key sharing among QKD links, a capability unattainable using existing technologies. Through comprehensive evaluations, we validate the benefits of PQNMs and demonstrate the efficacy of the presented strategies under various circumstances. Extensive results provide insightful resources for building QKD-enabled NMs in practice.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Giving Research Software Engineers a Larger Stage Through the Better Scientific Software Fellowship

The Better Scientific Software Fellowship (BSSwF) was launched in 2018 to foster and promote practices, processes, and tools to improve developer productivity and software sustainability of scientific codes. The BSSwF’s vision is to grow the community with practitioners, leaders, mentors, and consultants to increase the visibility of scientific software. Over the last five years, many fellowship recipients and honorable mentions have identified as research software engineers (RSEs). Furthermore, case studies from several of the program’s participants illustrate the diverse ways the BSSwF has benefited both the RSE and scientific communities. In an environment where the contributions of RSEs are too often undervalued, we believe that programs such as the BSSwF can help recognize and encourage community members to step outside of their regular commitments and expand on their work, collaborations, and ideas for a larger audience.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

2023 FORCE Development Status Update

Technical and economic analysis of integrated energy systems (IES) using software models is a complex process requiring multiple commodity market decision analysis, optimal control, process modeling, and stochastic analysis. Many assumptions used in traditional energy analysis tools do not hold in future energy markets with significant storage and variable renewable energy sources (VRE), let alone with multiple commodity markets. Capturing these intricate elements for accurate techno-economic analysis of IES led to the development of the Framework for Optimization of ResourCes and Economics (FORCE) tool suite under the U.S. Department of Energy’s Integrated Energy Systems crosscutting technology program. With the aim of a full framework release in 2025, many improvements to the FORCE tool suite were developed in fiscal year 2023 (FY23). These improvements broadly fit into three focuses for development of FORCE: capability, accessibility, and reliability. Capability refers to the ability of FORCE to accurately model the technical and economic viability of various IES. Accessibility refers to ease-of-use for new and existing IES analysts to efficiently set up, analyze, and produce results using FORCE. Reliability refers to the consistency of the software, allowing consistency to analysis regardless of erstwhile changes to the software. In addition to many smaller changes, there are three major capability improvements in FORCE in FY23. In summary, FORCE developments in FY23 have moved us close to all the capability requirements for FORCE 1.0 to be delivered in FY25. Inclusion of Bayesian optimization, resilience metrics, and levelized cost analysis expand the capability, accessibility, and reliability of FORCE.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2022

Automated Process Planning for Embossing and Functionally Grading Materials via Site-Specific Control in Large-Format Metal-Based Additive Manufacturing

The potential for site-specific, process-parameter control is an attribute of additive manufacturing (AM) that makes it highly attractive as a manufacturing process. The research interest in the functionally grading material properties of numerous AM processes has been high for years. However, one of the issues that slows developmental progress in this area is process planning. It is not uncommon for manual programming methods and bespoke solutions to be utilized for site-specific control efforts. This article presents the development of slicing software that contains a fully automated process planning approach for enabling through-thickness, process-parameter control for a range of AM processes. The technique includes the use of parent and child geometries for controlling the locations of site-specific parameters, which are overlayed onto unmodified toolpaths, i.e., a vector-based planning approach is used in which additional information, such as melt pool size for large-scale metal AM processes, is assigned to the vectors. This technique has the potential for macro- and micro-structural modifications to printed objects. A proof-of-principle experiment is highlighted in which this technique was used to generate dynamic bead geometries that were deposited to induce a novel surface embossing effect, and additional software examples are presented that highlight software support for more complex objects.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Models For Automated Screening Of Condition Report

As part of the corrective action program (CAP) at nuclear power plants, employees are given the opportunity and responsibility to identify issues and conditions present at the plant that may have an effect on the function of plant systems. When an employee identifies a potential issue, they create a condition report which is submitted to the CAP system. This condition report then goes through a screening process to determine the importance of the condition and thus the priority that must be placed on correcting it and/or preventing future issues. The purpose of this software is to assist with the screening process in an automated way using machine learning models. This software covers both the training of a machine learning model as well as applying the model to records.

Krome, Cameron↗
DOE OSTI2022

Real-Sim Interface: Enabling Multi-resolution Simulation and X-in-the-Loop Development for Connected and Automated Vehicles

We report connected and automated vehicles (CAVs) can bring safety, mobility, and energy benefits to transportation systems. Ideally, CAV applications would be fully evaluated and validated prior to real-world implementation. However, many technical challenges in both software and hardware hinder the process. To comprehensively evaluate all aspects of CAV applications, an integrated evaluation environment is needed with various simulation tools from different domains. In the current literature, there lacks a well-developed interface to enable multi-resolution simulation of vehicle, traffic, virtual environment, and hardware-in-the-loop (HIL) simulation. In this work, a modular and flexible interface is developed to enable multi-resolution vehicle and traffic co-simulation for CAV applications. This interface is built upon Oak Ridge National Laboratory’s (ORNL’s) Real-Sim approach, can support various simulation tools and real-time X-in-the-loop (XIL) simulations, and is based on network communication protocols. The network communication delays are analyzed for simultaneous connection of up to 20 simulators. Then, two example applications are studied to demonstrate the potential usage of the Real-Sim interface: (1) a centralized merging scenario where the dynamics of two ego vehicles are emulated with detailed vehicle and powertrain dynamics models and (2) a signal-controller-in-the-loop (SCIL) evaluation where one intersection of the simulated traffic scenario is controlled by a physical signal controller. This Real-Sim interface is a tool that allows researchers to bring real, tangible hardware and software into simulated environments to comprehensively evaluate and support a wide variety of CAV applications.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2019

SKA shakes hands with Summit

Recently, a full-scale data processing workflow (Fig. 1) of the Square Kilometre Array (SKA) Phase 1 was successfully executed on the world’s fastest supercomputer Summit, proving that scientists have the expertise, software tools and computing resources to process the SKA data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Inference-Engine v0.1.0

Given a pre-trained neural network, Inference-Engine performs maps network inputs to outputs by executing the forward pass through the provided network. Although the predominant programming language for machine-learning is Python, most high-performance computing (HPC) applications are written in Fortran, C, or C++. Inference-Engine aims to support HPC programs and is written in Fortran, a language with a large feature set supporting interoperability with C. This software exposes concurrency in a portable way by using standard language features that some modern Fortran compilers can exploit with various optimizations, including offloading computation to a Graphics Processing Unit (GPU). In particular, this software makes extensive use of Fortran's "do concurrent" parallel loop construct, implicitly parallel array statements, and pure procedures that can be invoked inside "do concurrent" blocks. Inference-Engine also supports dynamic choice of inference methods at runtime. Two current options include one method that uses Fortran's "dot_product" intrinsic function inside "do concurrent" blocks and another method that instead uses Fortran' "matmul" array intrinsic function. We plan to investigate automatic compiler offloading of "do concurrent" calculations to GPUs and compile-time substitution of optimized libraries such as the Basic Linear Algebra Library (BLAS) for "matmul" invocations. We also envision the potential for the choice of which method to use could happen at program launch based on in situ performance measurements on any given platform.

Rouson, Damian↗
DOE OSTI2025

stor4build

The EnergyPlus simulation engine supports modeling and simulation of thermal energy storage (TES) systems in several ways, including using the Python-EMS feature, which extends the operation of the engine with custom code written in Python. Creation of models using this feature can be tedious and error prone, with the connection of the model components to the Python code a particularly troublesome area. The stor4build Python package simplifies this process by modifying an input model to add a selected TES technology (implemented with the Python-EMS feature) and runs the simulation. The package leverages the OpenStudio middleware software development kit to automate this process as much as possible, eliminating potential errors and simplifying usage of EnergyPlus. The package provides objects, functions, and OpenStudio measures that implement the necessary operations to automate the creation of EnergyPlus models that integrate TES technologies with building systems. In addition, two user interfaces are provided: a command line interface and a web application programming interface. The automated process implemented by the package greatly simplifies the modeling and simulation process, allowing for parametric studies to be executed much more efficiently and effectively. The OpenStudio-based workflow is also very flexible and will allow for future additions of new technologies.

DeGraw, JasonWilliam [Oak Ridge National Laborator↗
DOE OSTI2021

Electrochemically Engineered, Highly Energy-Efficient Conversion of Ethane to Ethylene and Hydrogen below 550 °C in a Protonic Ceramic Electrochemical Cell

Ethylene is one of the largest building blocks in the petrochemical industry, mainly produced by steam cracking of ethane derived from naphtha or shale gas at high temperatures (>800 °C). Despite its technical maturity and economic competitiveness, the thermal steam cracking of ethane is highly energy-intensive. In this work, an electrochemically engineered direct conversion process of ethane to produce hydrogen and ethylene using a planar protonic ceramic membrane reactor with a bi-functional three-dimensional catalytic electrode is reported, with a single-pass ethane conversion of 40% and ethylene yield of 26.7% at 550 °C. Compared with the industrial ethane steam cracking, this method saves process energy input by 45.1% and improves process energy efficiency by 50.6%, based on comprehensive process simulation using Aspen Plus software. Further, steam electrolysis treatment under the solid oxide electrolysis cell mode can regenerate the system’s catalytic performance and significantly alleviate catalytic degradation by 74%, demonstrating high techno-economic viability.

bi-functional electrode↗
DOE OSTI2021

Cognitive analysis of metabolomics data for systems biology

Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researchers, but new NLP tools are emerging for biologists in other fields and an important example is metabolomics. NLP provides literature-based contextualization of metabolic features that decreases the time and expert-level subject knowledge required during the prioritization, identification and interpretation steps in the metabolomics data analysis pipeline. Here, we describe and demonstrate four workflows that combine metabolomics data with NLP-based literature searches of scientific databases to aid in the analysis of metabolomics data and their biological interpretation. Additionally, the four procedures can be used in isolation or consecutively, depending on the research questions. The first, used for initial metabolite annotation and prioritization, creates a list of metabolites that would be interesting for follow-up. The second workflow finds literature evidence of the activity of metabolites and metabolic pathways in governing the biological condition on a systems biology level. The third is used to identify candidate biomarkers, and the fourth looks for metabolic conditions or drug-repurposing targets that the two diseases have in common. The protocol can take 1–4 h or more to complete, depending on the processing time of the various software used.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Integrative Quantitative-Phase and Airy Light-Sheet Imaging

Light-sheet microscopy enables considerable speed and phototoxicity gains, while quantitative-phase imaging confers label-free organelle recognition and metabolic information that are inaccessible by conventional methods. We report the fusion of these two modalities onto a standard inverted microscope that retains compatibility with microfluidics. We describe the utilization of an accelerating Airy-beam light-sheet yielding identical imaging areas with interferometry, and an application in unmasking the effects of cellular noise on metabolic compartmentalization.

Biological sciences, Biological techniques, Micros↗
DOE OSTI2021

X-ray multi-probe data acquisition: A novel technique for laser pump x-ray transient absorption spectroscopy

We report the development and implementation of a novel data acquisition (DAQ) technique for synchrotron-based laser pump X-ray Transient Absorption (XTA) spectroscopy, called X-ray Multi-Probe DAQ (XMP DAQ). This technique utilizes high performance analog to digital converters and home-built software to efficiently measure and process the XTA signal from all x-ray pulses between laser excitations. XMP DAQ generates a set of time resolved x-ray absorption spectra at thousands of different pump–probe time delays simultaneously. Two distinct XMP DAQ schemes are deployed to accommodate different synchrotron storage ring filling patterns. Current Integration (CI) DAQ is a quasi-analog technique that implements a fitting procedure to extract the time resolved absorption intensity from the averaged fluorescence detector response. The fitting procedure eliminates issues associated with small drifts in the voltage baseline and greatly enhances the accuracy of the technique. Photon Counting (PC) DAQ is a binary technique that uses a time resolved histogram to calculate the XTA spectrum. While PC DAQ is suited to measure XTA data with closely spaced x-ray pulses (~10 ns) and a low count rate (<1 detected photon/pulse), CI DAQ works best for widely spaced pulses (tens of ns or greater) with a high count rate (>1 detected photon/pulse). XMP DAQ produces a two-dimensional XTA dataset, enabling efficient quantitative analysis of photophysical and photochemical processes from the sub-nanosecond timescale to 100 μs and longer.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Ground and excited state gradients with end-to-end differentiable semiempirical quantum chemistry

Accurate and efficient gradients of molecular energy with respect to nuclear degrees of freedom are essential for geometry optimization and molecular dynamics, including simulations that go beyond the Born–Oppenheimer regime. A common approach involves deriving analytical formulas for new electronic structure methods, which is often conceptually difficult and requires tedious coding. Here, we implement analytical, semi-numerical, and automatic differentiation (AD)-based gradient pathways for semiempirical Hamiltonian models in the PYSEQM software package, leveraging both graphics processing unit (GPU) and central processing unit (CPU) architectures. We further extend these capabilities to excited states calculated using the configuration interaction singles and time-dependent Hartree–Fock ansätze. We benchmark wall time, peak memory usage, and accuracy across three molecular families of varying chemical complexity, including systems of up to a thousand atoms. For ground-state simulations, analytical and AD gradients achieve near-identical GPU runtimes, while semi-numerical gradients are slower on GPU but remain competitive on CPU. For excited states, both analytical and custom AD approaches using implicit differentiation show similar performance and low memory requirements, whereas gradients with full AD are memory-limited. AD gradients match analytical ones in accuracy across all tested systems, aided by a quaternion-based diatomic frame rotation for two-center quantities that ensures smooth energy surfaces. Overall, automatic differentiation emerges as a practical alternative to analytical gradients in semiempirical quantum chemistry, offering high accuracy while allowing seamless integration in AI-driven workflows and popular packages, such as PyTorch and JAX. Our results provide actionable guidance for selecting optimal gradient strategies in large-scale ground- and excited-state molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A crystal plasticity finite element method modeling of Zircaloy with hydride phases based on scanning electron micrographs

This work developed a microstructure-based finite element model to predict the stress state of alloys with second phase inclusions. Quantitative microstructural details extracted from scanning electron microscopy (SEM) images were used to generate heterogeneous microstructures including the morphology and spatial distribution of hydrides. Generation of digital microstructure was achieved through two steps of tessellations using software Neper and Matlab. The process is demonstrated using an example of Zircaloy material with secondary phases of hydrides dispersed within and stress-strain response of Zircaloy containing hydrides was predicted. The constitutive material model for Zircaloy in this study was based on crystal plasticity theory which considers the hexagonal close-packed (HCP) atomic structure of Zircaloy material. The hydrides were modeled as isotropic elasto-plastic material. A parametric study had been conducted to understand the effect of volume fraction, and lamellae thickness of the hydride phase on the mechanical properties of the overall material. Results can help designers to alter the manufacturing process to obtain the enhanced mechanical properties for components used in nuclear applications made by Zircaloy material.

Kulkarni, Shank S.↗