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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Improving the Discovery Power of the Dark Energy Survey Gravitational Wave Program in Its Fourth Observing Campaign

The universe is growing at an accelerated rate, yet the several experiments and science cases used to measure this property yield conflicting results for the rate. Known colloquially as the Hubble tension problem, this discrepancy calls for a novel measurement of the Hubble Constant, H0, in order to be resolved. The Dark Energy Survey Gravitational Wave group (DESGW) aims to relieve this tension by performing a standard sirens measurement of H0 independent of traditional methods. To do so in the current era of data abundance and limited telescope time demands a robust, optimized, and complete science software pipeline to carefully balance the transition from gravitational wave data to state-of-the-art images, images to photometric data, and photometric data to identification and analysis of electromagnetic counterparts to gravitational wave signals. This thesis details the contributions of the author to the DESGW Search & Discovery Pipeline for the fourth observing run of the LIGO/Virgo/KAGRA gravitational wave detector network, as well as the science applications that have been pursued.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Future Trends in Nuclear Physics Computing

In nuclear physics (NP) today the study of quarks, gluons and their strong interactions extends across a broad research program at a varied range of collaborative scales, from a few collaborators up to large experiments at scales comparable to those typical of high energy physics (HEP). Overall, the software and computing efforts vary accordingly, from pragmatic do-it-yourself approaches among a few, to substantial organized software and computing activities within large experiments. With new experiments starting up and on the horizon [1], and rapidly increasing data volumes [2, 3] and processing demands even at small experiments, the NP community has in recent years been thinking about the next generation of data processing and analysis workflows that will maximize the science output. One context for this discussion has been a series of workshops, “Future Trends in Nuclear Physics Computing” [4]. The most recent in this series took place in Fall 2020, organized by the authors together with colleagues. The workshop focused on identifying the unique aspects of software and computing in NP, and discussing how the NP community could strengthen common efforts and chart a path forward for the next decade, sure to be an exciting one with rich ongoing scientific programs at Brookhaven National Laboratory (BNL), Jefferson Lab (JLab), and other NP facilities, and culminating in datataking at the Electron-Ion Collider (EIC) [5,6,7] in the early 2030s. Without claiming to present a collective view from the workshop and discussions since—fortunately this is not expected of us in this opinion editorial—we offer here our reflections on the topic, informed by the workshop and the summary we authored with our colleagues [8], as well as discussions and developments in the eventful time since.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Ultrahigh performance LC/FT-MS non-targeted screening for biomass burning organic aerosol with MZmine2 and MFAssignR

In recent years, ultrahigh performance liquid chromatography Fourier transform mass spectrometry (LC/FT-MS) based non-targeted screening (NTS) methods have become increasingly popular for comprehensive analysis of complex organic mixtures. However, applying these methods for environmental complex mixture analysis is challenging due to the extreme complexity of natural samples and a lack of standard samples or surrogates for environmental complex mixtures. Furthermore, limited molecular markers in the databases and insufficient data processing software workflows make the application of these methods more challenging for environmental complex mixtures. In this work, we implement a new NTS data processing workflow to process data collected from ultrahigh performance liquid chromatography and Fourier transform Orbitrap Elite Mass Spectrometry (LC/FT-MS) by combining MZmine2 and MFAssignR, two opensource data processing tools and commercial Mesquite liquid smoke as a surrogate for biomass burning organic aerosol. MZmine2.53 data extraction followed MFAssignR molecular formula assignment offered noise free and highly accurate 1733 individual molecular formulas presented in liquid smoke with 4906 molecular species, including isomers. The results of this new approach were consistent with the results of direct infusion FT-MS analysis confirming its reliability. Over 90% of the molecular formulas presented in mesquite liquid smoke were matched with the molecular formulas of ambient biomass burning organic aerosol. This suggests the potential use of commercial liquid smoke as a surrogate for biomass burning organic aerosol research. Furthermore, the presented method significantly improves the identification of the molecular composition of biomass burning organic aerosol by successfully addressing some of the limitations related to the data analysis and giving a semi quantitative insight into the analysis.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

What's in a Name? Developing a Standardized Taxonomy for HVAC System Faults

Faults occurring in heating, ventilation and air-conditioning (HVAC) systems have significantly negative impacts on building energy consumption, occupant comfort, and indoor air quality. In the past thirty years, extensive research has been conducted on fault detection and diagnostics (FDD) methods, and there are now dozens of commercially available FDD software tools. Growing adoption of FDD tools has the potential to generate a massive and useful data set on fault characteristics. However, the lack of a unifying taxonomy is a significant barrier to efficient analysis and evaluation of FDD outputs. Therefore, there is a strong need to develop a robust taxonomy which can better represent and interpret FDD output data. This paper documents the development of a unifying taxonomy for HVAC system faults in commercial buildings, with initial focus on air handling units, variable air volume terminal units, and roof top unit systems. The developed fault taxonomy employs both a physical hierarchy of HVAC equipment and a cause-effect relationship model as tools to better understand and support root cause analysis for HVAC faults. A variable air volume terminal unit is used as an example to demonstrate the application of the developed fault taxonomy. The taxonomy has short-term application in a major U.S. study on fault prevalence, and promises longer term benefits to FDD software developers and building operators by creating a foundation for improved approaches to identifying and resolving HVAC faults.

Chen, Yimin↗
DOE OSTI2020

Fire Risk Investigation in 3D (FRI3D) Software and Process for Integrated Fire Modeling

Modeling and implementing fire safety for nuclear power plants is a costly activity. Because of the complexity of fire phenomena and multiple operational procedures, it is difficult to computationally provide assurance that mitigation methods are adequate for critical areas using current analysis methods in a cost-effective manner. The nuclear industry needs efficient methods to provide more accurate modeling and optimize mitigation methods to improve nuclear power plant understanding for fire scenarios. This report describes the work done over the last two year on the Fire Risk Investigation in 3D (FRI3D) software. This software simplifies the modeling process by importing existing plant models and data, incorporating a 3D modeling environment and coupling with the fire simulation software CFAST. This eliminates the manual labor and errors associated with much of the fire modeling process. The report lays out the status and path of FRID software for the Risk Informed Safety Analysis pathway of the Light Water Reactor Sustainability project at Idaho National Laboratory and industry collaborators to best help reduce costs and improve realism in fire probabilistic risk analysis.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Insufficient reporting of x-ray photoelectron spectroscopy instrumental and peak fitting parameters (metadata) in the scientific literature

This study was motivated by earlier observations. It is a systematic examination of the adequacy of reporting of information (metadata) necessary to understand x-ray photoelectron spectroscopy (XPS) data collection and data analysis in the scientific literature. The information for this study was obtained from papers published in three high-quality journals over a six-month period in 2019 and throughout 2021. Each paper was evaluated to determine whether the authors had reported (percentages of the papers properly providing the information are given in parentheses) the spectrometer (66%), fitting software (15%), x-ray source (40%), pass energy (10%), spot size (5%), synthetic peak shapes in fits (10%), backgrounds in fits (10%), whether the XPS data are shown in the main body of the paper or in the supporting information (or both), and whether fitted or unfitted spectra were shown (80% of published spectra are fit). The Shirley background is the most widely used background in XPS peak fitting. The Al Kα source is the most widely used x-ray source for XPS data collection. CASAXPS is the most widely used fitting program for XPS data analysis. Further, there is good agreement between the results gathered during the two years of our survey. There are some hints the situation may be improving. This study also provides a list of the information/parameters that should be reported when XPS is performed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

X-composer: enabling cross-environments in-situ workflows between HPC and cloud

As large-scale scientific simulations and big data analyses become more popular, it is increasingly more expensive to store huge amounts of raw simulation results to perform post-analysis. To minimize the expensive data I/O, "in-situ" analysis is a promising approach, where data analysis applications analyze the simulation generated data on the fly without storing it first. However, it is challenging to organize, transform, and transport data at scales between two semantically different ecosystems due to the distinct software and hardware difference. To tackle these challenges, we design and implement the X-Composer framework. X-Composer connects cross-ecosystem applications to form an "in-situ" scientific workflow, and provides a unified approach and recipe for supporting such hybrid in-situ workflows on distributed heterogeneous resources. X-Composer reorganizes simulation data as continuous data streams and feeds them seamlessly into the Cloud-based stream processing services to minimize I/O overheads. For evaluation, we use X-Composer to set up and execute a cross-ecosystem workflow, which consists of a parallel Computational Fluid Dynamics simulation running on HPC, and a distributed Dynamic Mode Decomposition analysis application running on Cloud. Our experimental results show that X-Composer can seamlessly couple HPC and Big Data jobs in their own native environments, achieve good scalability, and provide high-fidelity analytics for ongoing simulations in real-time.

Wang, Dali↗
DOE OSTI2021

CSPlib - A Software Toolkit for the Analysis of Dynamical Systems and Chemical Kinetic Models

CSPlib is an open source software library for analyzing general ordinary differential equation (ODE) systems and detailed chemical kinetic ODE systems. It relies on the computational singular perturbation (CSP) method for the analysis of these systems. The software provides support for: General ODE models (gODE model class) for computing source terms and Jacobians for a generic ODE system; TChem model (ChemElemODETChem model class) for computing source term, Jacobian, other necessary chemical reaction data, as well as the rates of progress for a homogenous batch reactor using an elementary step detailed chemical kinetic reaction mechanism. This class relies on the TChem [2] library; A set of functions to compute essential elements of CSP analysis (Kernel class). This includes computations of the eigensolution of the Jacobian matrix, CSP basis vectors and co-vectors, time scales (reciprocals of the magnitudes of the Jacobian eigenvalues), mode amplitudes, CSP pointers, and the number of exhausted modes. This class relies on the Tines library; A set of functions to compute the eigensolution of the Jacobian matrix using Tines library GPU eigensolver; A set of functions to compute CSP indices (Index Class). This includes participation indices and both slow and fast importance indices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Block Island Acoustic Propagation Modeling Data

This dataset contains acoustic propagation model outputs, computational subroutines, and analysis tools for underwater sound propagation in the Block Island region, including parabolic equation (PE) model results, visualization products, and comprehensive modeling software tools.

17 WIND ENERGY↗
DOE OSTI2024

A Survey of Open-Source Tools for Transmission and Distribution Systems Research

This work presents a review of open-source electric power transmission and distribution systems analysis tools suitable for use by industry professionals and academic researchers. Due to the high complexity of the electric grid, there exist numerous tools and extensive research pertaining to nearly every aspect of the design, operation, and control of transmission and distribution networks. In addition to the commercial tools, a wide range of free, open-source tools, models, and data usable by the scientific community for related research have been developed by different organizations, including both international and US universities and national laboratories. However, due to the absence of a catalog of available tools, models and data, researchers often lack a knowledge of existing capabilities and may develop duplicative software and tools. Increasing awareness of these available resources seeks to accelerate their broader use, leading to more efficient and standardized grid analysis. This review paper (which is part of a larger survey effort that studied over 400 tools in the transmission, distribution, buildings, and electric vehicles space) outlines selected open-source resources that have been developed in power transmission and distribution systems research. It is anticipated that this work can serve as a guide for industry and academic researchers alike, ensuring that research efforts are well-channeled.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2020

Comparison of gamma-ray spectral analysis methods for thick-walled UF 6 cylinders

Three data analysis methods were compared for gamma ray spectra collected by planar and coaxial high-purity germanium detectors (HPGe) on thick-walled uranium hexafluoride cylinders. The cylinder contents range from natural to low-enriched uranium (4.95% 235 U). Each spectrum was analyzed with the traditional 185.7 keV enrichment meter method, a 185.7/1001 keV ratio method, and the Fixed Energy Response Function Analysis with Multiple Efficiency (FRAM) software that utilizes low- and high-energy gamma rays and X-rays. When results for all cylinders were compared, the enrichment meter method and the 185.7/1001 keV peak ratio method consistently provided the most accurate data for all detector types. The error on the enrichment calculations analyzed with FRAM did not meet the international target value whereas those calculated with the enrichment meter and ratio method did. Enrichments calculated by FRAM were found to skew to higher values on natural uranium and to lower values on low-enriched uranium. FRAM calculated the least-precise enrichments; replicate analyses of single cylinders resulted in 235 U values that varied by as much as 19%. FRAM does have the significant advantages in that it does not require the use of calibration cylinders, infinite thickness criteria are not necessary, and it can be applied to any HPGe detector. Finally, if calibration cylinders are available, the enrichment meter and 185.7/1001 peak ratio are the recommended methods as they are the most accurate and precise.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

A novel integrated time-resolved array avalanche photodiode detection system for nuclear resonant scattering measurements

Here, the nuclear resonant scattering (NRS) experiment requires photon-counting detectors with high time resolution, short dead time, large dynamic range, low noise, and large detection area. An 8-channel avalanche photodiode (APD) array detector system with high integrity, flexibility, and reliability has been developed to adapt to the demands of NRS experiments. The detector system mainly consists of four key parts: (i) an array-APD sensor, (ii) 8-channel integrated fast preamplifiers, (iii) the time-to-digital converter readout electronics, and (iv) a data acquisition system and EPICS support software. Remarkably, the system exhibits a time resolution of better than 500 ps and has a sufficiently low noise level, allowing for the lowest detection energy threshold of 4 keV. The performance of the new array-APD system as well as its real application in nuclear forward scattering (NFS) and nuclear resonant inelastic x-ray scattering (NRIXS) experiments was tested in two synchrotron facilities. With the new system, the NFS signal very close to the prompt electronic scattering signal can be extracted. Thanks to the customized EPICS-areaDetector-based control software, NRIXS spectra can be readily measured with time and energy information of the NRIXS signal stored in the raw data, which is promising for developing NRIXS data analysis in the time domain. The array-APD detector can be deployed for nuclear resonant scattering experiments at various synchrotron radiation facilities.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

wastewater_virus

This repo contains software used to clean and assemble high-throughput sequencing data containing viruses. The input is raw illumina sequencing reads and the output is a database of high-quality viral genomes. The specific application is to wastewater viral concentrates but it is not restricted to that sample type. The software is composed of Nextflow workflows and a set of custom Python and bash scripts that call publicly available bioinformatics tools to accomplish obvious tasks in data analysis in a high performance computing environment. For detailed information, please see the repo's README file.

Kantor, Rose [Lawrence Livermore National Laborato↗
DOE OSTI2025

Establishing model credibility for process-microstructure-property relationships in additive manufacturing using exascale computing

Additive Manufacturing (AM) of alloys holds significant promise as a disruptive technology in various industries, yet its adoption is often hindered by challenges in achieving consistent part quality. These issues are primarily due to the complex process-microstructure-property (PSP) relationships inherent to AM. Computational models can greatly aid in understanding these relationships, but their widespread impact and adoption has been limited by a lack of validated, open-source, and computationally efficient PSP modeling frameworks and hardware limitations. Here, this study leverages the ExaAM software suite and data from the AMBench-2018 series of laser powder bed fusion (LPBF) benchmark experiments to perform a comprehensive model assessment, including verification, validation, sensitivity analysis, and uncertainty quantification. The RADICAL-EnTK workflow manager was used to perform an ensemble of heat transport, solidification, and mechanical response simulations on the exascale computer Frontier, considering uncertainties in critical model inputs such as laser spot size and nucleation parameters, and consisting of 125 explicit grain structure simulations and 7875 crystal plasticity simulations. For a selected location within the Inconel 625 AMBench-2018 test artifact, sensitivity analysis and uncertainty quantification were performed using the predicted distributions of grain structure and mechanical properties. Qualitative agreement was found between the predicted grain size and texture and the observed AMBench-2018 microstructure, the mean predicted yield stress was within 5% of the experimental measurement mean, and the mean predicted engineering stress at 5% strain was within 10% of the experimental measurement mean. The insights gained from development and validation of the ExaAM PSP modeling framework will help guide future directions for enhancing the credibility and reliability of PSP models in AM, thereby accelerating the adoption of AM technologies in various industries.

Additive manufacturing↗
DOE OSTI2023

Modeling Non-UO2 Fuel With UNF-ST&DARDS

The U.S. Department of Energy’s Used Nuclear Fuel-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS) provides an easy-to-use interface to analyze irradiated UO2 fuel by allowing all analysis to be performed within the software and being able to store and use dozens of fuel assembly, canister, and cask designs [1]. However, performing these same analyses with non-UO2 fuel, such as UN or U3Si2, requires more user intervention in the process. This work uses UN, UN-ZrO2, and U3Si2 fuel to demonstrate how to perform criticality analyses in the current versions of UNF-ST&DARDS and how a non-UO2 fuel will compare to UO2. This work is part of a larger effort that also includes shielding and thermal analyses, but they will not be discussed.

Ivanusa, Pavlo↗
DOE OSTI2026

PlantCV v4: Image analysis software for high‐throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.

Schuhl, Haley [Donald Danforth Plant Science Cente↗
DOE OSTI2026

Evaluation of Hardware and Software Bill of Materials (HBOMs/SBOMs) Extraction Methods

Hardware and software bills of materials (HBOMs and SBOMs) provide important visibility into the components, dependencies, and supply chain relationships within programmable digital devices. This visibility is critical for advanced nuclear reactor applications, where use of common or shared hardware components, software libraries, suppliers, or manufacturing processes may create common cause failure (CCF) vulnerabilities despite apparent diversity. This paper evaluates current approaches for obtaining and analyzing HBOMs and SBOMs in support of CCF, diversity and defense-in-depth (D3) assessments, and begins to explore potential methods for artificial intelligence/machine learning-based analysis. The availability of BOM information from advanced reactor manufacturers and vendors, representative hardware and software categories found in advanced reactor systems continues to limit research [13]. This paper compares commonly used BOM formats, including CycloneDX, SPDX, and SWID. It also surveys publicly available tools for generating BOMs from source code, compiled binaries, and hardware-related information, noting limitations in language coverage, system age, and format interoperability. Finally, this paper evaluates methods for correlating BOM data with vulnerability and exploitability information, including VEX, CVE, and CWE resources. The findings indicate that publicly available nuclear-vendor BOMs are limited, making third-party extraction and research into novel analysis techniques necessary.

Cybersecurity↗
DOE OSTI2022

Next generation experimental data access at NSLS-II

The NSLS-II network and computing infrastructure has been significantly updated recently. The re-IP process in 2020-2021 enabled the NSLS-II network to be routable to the rest of the BNL campus. Then, standardization of the operating systems and deployment procedures helped to deliver a consistent environment to workstations and servers used by all NSLS-II beamlines. In particular, the RedHat Enterprise Linux 8 was deployed to 700+ machines using the RedHat Satellite infrastructure management product, and all critical services (IOCs, databases, etc.) were migrated to the new OS. NFS users’ home directories are consistent across all of the machines, which eliminates the need for the individual configuration of the user environment on each host. The standard suite of software packages is available to the beamline staff and users, which includes the system packages (deployed via RPM) as well as the conda environments for data acquisition and analysis. Security measures were implemented to comply with the industry standards, which include multi-factor authentication (using Duo), secure screen lock for the beamline machines, and advanced access control to the experimental data that is stored in shared central storage available on all hosts. These major enhancements facilitated sharing the experimental data (currently for a number of selected beamlines, with a plan to extend it to the whole facility in the nearest future) with the users via an externally facing JupyterHub instance. The beamlines keep using the Bluesky data acquisition framework to orchestrate their experiments, and the new infrastructure enabled them to use a next-generation data access library called tiled.

36 MATERIALS SCIENCE↗