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DOE OSTI2023

mzapy : An Open-Source Python Library Enabling Efficient Extraction and Processing of Ion Mobility Spectrometry-Mass Spectrometry Data in the MZA File Format

We have recently reported MZA, a new and simple mass spectrometry data structure based on the broadly supported HDF5 format and created to facilitate software development. While this format is inherently supportive of application development, the availability of a core library with standard mass spectrometry utilities greatly facilitates fast software development. Here, we present a Python library, mzapy, for efficient extraction and processing of mass spectrometry data in the MZA format. In addition to raw data extraction, mzapy contains supporting utilities enabling tasks including calibration, signal processing, peak finding, and generating plots. Being implemented in pure Python with minimal and largely standardized dependencies makes mzapy uniquely suited to application development in the multi-omics domain. The free and open source mzapy is built with extensibility in mind, and future development will support cloud computing and artificial intelligence/machine learning applications. The software source code is freely available at https://github.com/PNNL-m-q/mzapy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

ARGONNE DISCOVERY CLOUD SDK&CLI

Software development kit and command-line interface to access and interact with the Argonne Discovery Cloud platform. Software code can be used to enable software developers to add their own integrates into their own software.

AVARCA, ANTHONY↗

DOE OSTI2018

Development of Software Defined Radio Protocol for Acoustic Communication on Pipes

Nuclear Science Engineering Division at Argonne has been developing a new method of transmitting information via acoustic waves on pipes in a nuclear facility. This method provides the capability to communicate information from within the containment building under the conditions of total power outage following a severe accident. Compared to traditional RF communications, acoustic communications allows for signal transmission across thick concrete barriers, and better information security due to spatial confinement of the signal. Data of interest consists of sensor readings, voice, and images. Transmission of images is most challenging because corruption of the header string might render the reconstructed image unreadable.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Enhanced Data Efficiency Using Deep Neural Networks and Gaussian Processes for Aerodynamic Design Optimization

Adjoint-based optimization methods are attractive for aerodynamic shape design primarily due to their computational costs being independent of the dimensionality of the input space and their ability to generate high-fidelity gradients that can then be used in a gradient-based optimizer. This makes them very well suited for high-fidelity simulation based aerodynamic shape optimization of highly parametrized geometries such as aircraft wings. However, the development of adjoint-based solvers involve careful mathematical treatment and their implementation require detailed software development. Furthermore, they can become prohibitively expensive when multiple optimization problems are being solved, each requiring multiple restarts to circumvent local optima. In this work, we propose a machine learning enabled, surrogate-based framework that replaces the expensive adjoint solver, without compromising on predicting predictive accuracy. Specifically, we first train a deep neural network (DNN) from training data generated from evaluating the high-fidelity simulation model on a model-agnostic design of experiments on the geometry shape parameters. The optimum shape may then be computed by using a gradient-based optimizer coupled with the trained DNN. Subsequently, we also perform a gradient-free Bayesian optimization, where the trained DNN is used as the prior mean. We observe that the latter framework (DNN-BO) improves upon the DNN-only based optimization strategy for the same computational cost. Overall, this framework predicts the true optimum with very high accuracy, while requiring far fewer high-fidelity function calls compared to the adjoint-based method. Furthermore, we show that multiple optimization problems can be solved with the same machine learning model with high accuracy, to amortize the offline costs associated with constructing our models. Our methodology finds applications in the early stages of aerospace design. (C) 2021 Published by Elsevier Masson SAS.

Renganathan, S. Ashwin↗

DOE OSTI2026

Shadow of the Future: Developing Trust and Software within the Exascale Computing Project

Collaboration and team science are emerging areas of interest in software production. Historically, multi-institutional research collaborations are difficult to initiate and maintain, negatively impacting communication, negotiation, and dialogue between industry, government, and academic researchers. The Exascale Computing Project (ECP), a massive, multi-team, high-stakes initiative, facilitated broader research collaboration under a shared funding structure and extended timeline to support scientific discovery. Here, we conducted interviews with ECP teams, representing a variety of domain specialties, research institutions, and programming backgrounds. Using thematic analysis, we assessed how ECP’s structure created an environment of increased trust among projects and how software shared between teams facilitated sustained collaboration. We found that the expectation of future collaboration, i.e., the shadow of the future, greatly enhanced trust among teams and the quality of scientific software produced. Based on our findings within ECP projects, we connect to the existing literature on trust in software engineering and share recommendations for sustainable multi-institutional collaboration and shared best software practices.

Exascale computing project↗

DOE OSTI2015

The Monte Carlo estimation of an effect of uncertainties in initial data on solving the transport equation by means of the MCU code

A new version of the tally module of the MCU software package is developed in which the approach for taking directly into account the uncertainty in initial data is implemented that is recommended by the international standard on estimating the uncertainty in results of measuring (ISO 13005). The new module makes it possible to evaluate the effect of uncertainty in initial data (caused by technological tolerances in fabrication of structural members of the core) on neutronic characteristics of the reactor. The developed software is adapted to parallel computing with the use of multiprocessor computers, which significantly reduces the computation time: the parallelization coefficient is almost equal to 1. Testing is performed by examples of solving the problem on criticality for the Godiva benchmark experiment and also for the infinite lattice of fuel assemblies of the VVER-440, VVER-1000, and VVER-1200. The results of calculations of the uncertainty in neutronic characteristics (effective multiplication factor, fission reaction rate), which is caused by uncertainties in initial data due to technological tolerances, are compared (in the first case) to the published results obtained using the precision MCNP5 code and (in the second case) to those obtained by means of the RADAR engineering program. A good agreement of results is achieved for all cases.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2018

BESTEST-GSR (Building Energy Simulation Test - Generation Simulation and Reporting) [SWR 18-23]

Building Energy Simulation Test (BESTEST) is an NREL-developed method to validate the qualitative performance of different whole building simulations engines relative to each other. https://www.nrel.gov/docs/legosti/old/6231.pdf For EnergyPlus® and OpenStudio®, generation of test cases, simulation, and reporting has been a manual or partially automated process that typically took a number of months after a new version of EnergyPlus came out. Building Energy Simulation Test - Generation Simulation and Reporting (BESTEST-GSR) was developed to fully automate this process so it is less error-prone, less time-consuming, and can be quickly run on request for any development branch of EnergyPlus and OpenStudio. The initial use case is to directly support OpenStudio and EnergyPlus development, but the software is configured to support use by external software developers that build tools on top of EnergyPlus and/or OpenStudio. Tools built on top of OpenStudio can leverage the test generation, simulation, and reporting, while tools built on EnergyPlus can leverage the test simulation and reporting. The model generation is accomplished by running OpenStudio measures for envelope, heating, or cooling test cases. At this stage the specified weather file required for a specific test case is assigned to the model. Simulation is enabled using the OpenStudio Command Line Interface (CLI) to run a series of OpenStudio and Reporting measures to a specified seed model. The specified workflow is defined with an OpenStudio OSW file. The first measure generates the test case model, while the second measure is a reporting measure that runs after the simulation to collect necessary simulation results from the EnergyPlus SQL file. The Reporting stage gathers data from individual OpenStudio OSW files and populates a series of BESTEST Microsoft Excel spreadsheets. BESTEST-GSR also gathers zip files from individual simulations for diagnostic purposes.

Goldwasser, David↗

DOE OSTI2016

Large Scale Screening of Low Cost Ferritic Steel Designs For Advanced Ultra Supercritical Boiler Using First Principles Methods

Advanced Ultra Supercritical Boiler (AUSC) requires materials that can operate in corrosive environment at temperature and pressure as high as 760°C (or 1400°F) and 5000psi, respectively, while at the same time maintain good ductility at low temperature. We develop automated simulation software tools to enable fast large scale screening studies of candidate designs. While direct evaluation of creep rupture strength and ductility are currently not feasible, properties such as energy, elastic constants, surface energy, interface energy, and stack fault energy can be used to assess their relative ductility and creeping strength. We implemented software to automate the complex calculations to minimize human inputs in the tedious screening studies which involve model structures generation, settings for first principles calculations, results analysis and reporting. The software developed in the project and library of computed mechanical properties of phases found in ferritic steels, many are complex solid solutions estimated for the first time, will certainly help the development of low cost ferritic steel for AUSC.

36 MATERIALS SCIENCE↗

DOE OSTI2018

Developing Fugitive Emissions Sensor Networks

This document summarizes research performed under the Laboratory Directed Research and Development (LDRD) project titled Developing Fugitive Emissions Sensor Networks: New Optimization Algorithms for Monitoring, Measurement and Verification. The purpose of this project is to develop methods and software to enhance detection programs through optimal design of the sensor network. This project includes both software development and field work. While this project is focused on methane emissions, the sensor placement optimization framework can be applied to a wide range of applications, including the placement of water quality sensors, surveillance cameras, fire and chemical detectors. This research has the potential to improve national security by improving the way sensors are deployed in the field.

47 OTHER INSTRUMENTATION↗

DOE OSTI2018

When Data Analytics Meet Site Operation: Benefits and Challenges

Demand for using data analytics for energy management in buildings is rising. Such analytics are required for advanced measurement and verification, commissioning, automated fault-detection and diagnosis, and optimal control. While novel analytics algorithms continue to be developed, bottlenecks and challenges arise when deploying them for demonstration, for a number of reasons that do not necessarily have to do with the algorithms themselves. It is important for developers of new technologies to be aware of the challenges and potential solutions during demonstration. Therefore, this paper describes a recent deployment of an automated, physical model-based, FDD and optimal control tool, highlighting its design and as-operated benefits that the tool provides. Furthermore, the paper presents challenges faced during deployment and testing along with solutions used to overcome these challenges. The challenges have been grouped into four categories: Data Management, Physical Model Development and Integration, Software Development and Deployment, and Operator Use. The paper concludes by discussing how challenges with this project generalize to common cases, how they could compare to other projects in their severity, and how they may be addressed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

spot_bt v.0.1.1

SAND2024-08430O spot_bt allows users to easily construct complex, autonomous behaviors without having to overly rely on Boston Dynamic’s Spot robot software development kit. Using a form-of-state machine called a "behavior tree," the software develops and applies different "leaves" or actions to the robot. Attaching multiple actions in sequence creates a "branch," and a series of these make up the "tree." The software works on any x86 or aarch64 hardware but must run on a Linux OS. 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

Kakish, Zahi↗

DOE OSTI2016

Software Dependability for Digital Instrumentation and Control Systems in Nuclear Power Plants - Lessons Learnt from a DOE Sponsored Project

This paper discusses the lessons learnt from a sponsored study undertaken under the sponsorship of the Department of Energy by a team of scientists at the Ohio State University in collaboration with Technology Resources and experts around the world. This paper makes recommendations for future research and studies based on these lessons learnt. The purpose of the research was to provide a software dependability quantification framework that would allow its evaluation along the software development life cycle for safety critical instrumentation and control systems (I and C) such as those found in nuclear power plants. A typical example of safety critical system is the reactor protection system. The research funded by the Department of Energy built on preliminary research carried out for the US NRC that had focused solely on software reliability quantification. Quantification of software dependability is important for safety critical I and C because the regulatory framework in use in the United States for nuclear power plants is risk informed. Quantification of risk requires quantification of all contributors to risk and those include instrumentation and control systems. The purpose of the study was to help developers of software-based I and C with an early evaluation of the potential risk an application would represent at different stages of the software development life cycle by building gates at the end of each life cycle phase. Life cycle phases of software development comprehend phases such as requirements, design, coding and test. The gates' function would be to stop development from moving forward if the assessed dependability objective for that phase were not met. Gates thresholds were to be defined based on measurements collected during the life cycle phase under evaluation and phases that preceded it and an understanding of the mechanisms that would lead to threatening the dependability objectives. The information contained in the gates would in addition help steer the development towards areas that needed improvement. The following are four high level conclusions to our study. First the study demonstrates a lack of consensus on mechanisms that will threaten the dependability attributes. This lack of consensus should be resolved. The lack of consensus appears for all measures to the exception of reliability. Second, measures should be developed for software availability and safety. Third, for all dependability attributes (with the exception of reliability) consistency of the measurement threads should evaluated and measurement-based development gates derived. Finally our ability to perform such type of research depends in a significant manner on access to vendor and/or utility data. The licensing environment and the first-of-a-kind nature of current software-based applications for nuclear I and C make it difficult to collect the relevant data. An approach which would either increase access to data by providing 'immunity' to the vendor or utility or the development of a software-based I and C for the sole purpose of data collection for research should be investigated. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

FIC Vulnerability Profile

The FIC team is engaged with Pacific Northwest National Laboratory’s (PNNL’s) Shamrock Cyber Team to provide cybersecurity analyses of the FIC software. Shamrock offers both Threat-Based Analysis services and Secure Software Development services. These services are ultimately used to understand and mitigate threats against software and to reduce vulnerabilities in software, thus improving overall cybersecurity and informing decision makers. Shamrock’s Secure Software Development services, specifically Static Analysis Security Testing (SAST) and Open-Source Analysis (OSA), produced this Vulnerability Profile.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Standardizing UI/UX across accelerator labs

During February 26–28, 2025, the first-ever particle accelerator user interface/user experience (UI/UX) workshop was held at SLAC. Attendees had backgrounds ranging from software development to control systems management and human factors (HF) science. The workshop began with participants discussing the current state of UI/UX procedures and practices at their respective laboratories to share experiences and learn from one another. Additional discussions focused on how to effectively integrate UI/UX best practices into actionable goals for developers, managers, and operators when working on new or existing interfaces. The goal of the working group is to create a website that will guide developers, managers, scientists, and end users at accelerator laboratories in incorporating UI/UX best practices into software development. The working group continues to meet virtually toward this goal, and is planning a second workshop for next year.

Tran, Tiffany [SLAC]↗

DOE OSTI2015

Internal Indpendent Assessment Report - CASTLE-PX SQA

This IIA assessed the flow down of institutional 830 Software Quality Assurance requirements through three required document templates to the CASTLE-PX software effort and the implementation of those SQA requirements. The templates flow down the DOE O 414.1D consensus standard requirements for Safety Software. This assessment did not include the flow down of NAP-24, Weapon Quality Policy, requirements. The assessment focused on the CASTLE-PX project’s software development and release processes. It did not assess Pantex’s acceptance or usage of the software. The assessment resulted in 3 Deficiencies, 5 Observations, 1 Recommendation, and 3 Strengths. Overall the CASTLE-PX team demonstrated it values quality and has worked to integrate quality practices into its software development processes. Improvement in documentation will enhance their SQA implementation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Secure Design and Development Cybersecurity Capability Maturity Model (SD2-C2M2): Next-Generation Cyber Resilience by Design

The Secure Design and Development Cybersecurity Capability Maturity Model (SD2-C2M2) provides a browser-based tool that allows hardware and software developers to assess the maturity level of their design and development processes, allows management to determine desired maturity levels in seven domains, and allows developers to monitor process maturity improvements against management goals. The tool can be used by commercial developers as well as internal development organizations. This paper provides an overview of the tool and domains and presents a hypothetical case study of the tool to reduce software buffer overflow attack vulnerabilities by improving the software development process.

Gourisetti, Sri Nikhil G.↗

DOE OSTI2022

Challenges of and Opportunities for a Large Diverse Software Team

A large software team consisting of members with different expertise, skillsets, personalities, ethnicities, and involving collaboration on a large and complex software product presents many technical and cultural challenges, but also provides unique opportunities. In this article, we discuss the essential issues we faced when successfully transforming a collection of various independently developed software libraries into one large integrated product: the eXtreme-scale scientific Software Development Kit (xSDK). Furthermore, we argue it is just as important to pay attention to cultural challenges, such as establishment of reliable communication channels that considers, among others, differences in personalities and backgrounds as well as overcoming geographical separation and time-zone distribution when collaborating, as technical challenges. Finally, we discuss opportunities stemming from participating in a large diverse software team, such as increased internal expertise, variety of skillsets, broadened connections to external experts, and access to a larger pool of ideas or solutions.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

MOIS LabVIEW Software

Software developed in LabVIEW for the Modular Ocean Instrumentation System (MOIS) is provided. Two documents: MOIS User's Guide and MOIS Software Developer's Guide are included in the submission.

16 TIDAL AND WAVE POWER↗