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DOE OSTI2024

Integration of Waveform Simulation Methods

The generation of synthetic seismograms through simulation is a fundamental tool of seismology required to run quantitative hypothesis tests. A variety of approaches have been developed throughout the seismological community and each has their own specific user interface based on their implementation. This causes a challenge to researchers who will need to learn new interfaces with each new software they wish to use and create substantial challenges when attempting to compare results from different tools. Here we provide a unified interface that facilitates interoperability amongst several simulation tools through a modern containerized Python package. Further, this package includes post-processing analysis modules designed to facilitate end-to-end analysis of synthetic seismograms. In this report we present the conceptual guidance and an example implementation of the new Waveform Simulation Framework.

58 GEOSCIENCES↗

DOE OSTI2024

Sierra/SD – User's Manual – 5.22

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user’s guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Sierra/SD – User's Manual (V.5.24)

42 ENGINEERING↗

DOE OSTI2024

Evaluation of δ-Phase ZrH1.4 to ZrH1.7 Thermal Neutron Scattering Laws Using Ab Initio Molecular Dynamics Simulations

Zirconium hydride is commonly used for next-generation reactor designs due to its excellent hydrogen retention capacity at temperatures below 1000 K. These types of reactors operate at thermal neutron energies and require accurate representation of thermal scattering laws (TSLs) to optimize moderator performance and evaluate the safety indicators for reactor design. In this work, we present an atomic-scale representation of sub-stoichiometric ZrH2−x(0.3≤x≤0.6), which relies on ab initio molecular dynamics (AIMD) in tandem with velocity auto-correlation (VAC) analysis to generate phonon density of states (DOS) for TSL development. The novel NJOY+NCrystal tool, developed by the European Spallation Source community, was utilized to generate the TSL formulations in the A Compact ENDF (ACE) format for its utility in neutron transport software. First, stoichiometric zirconium hydride cross sections were benchmarked with experiments. Then sub-stoichiometric zirconium hydride TSLs were developed. Significant deviations were observed between the new δ-phase ZrH2−x TSLs and the TSLs in the current ENDF release. It was also observed that varying the hydrogen vacancy defect concentration and sites did not cause as significant a change in the TSLs (e.g., ZrH1.4 vs. ZrH1.7) as was caused by the lattice transformation from ϵ- to δ-phase.

42 ENGINEERING↗

DOE OSTI2022

AMSS

SAND2022-12902 O The Automated Method Selection Software (AMSS) is a chromatographic prediction tool based on the previously published BioCompound Machine Learning (BCML) tool. AMSS uses PubChem ID as input for molecule information such as SMILES and physical and chemical properties. The model is used to predict the best chromatography analysis method for testing compounds. 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.

Poorey, Kunal↗

DOE OSTI2020

Building commissioning costs and savings across three decades and 1500 North American buildings

B.V. Building commissioning (Cx) is a process for assuring efficient building operations that can be applied to new construction and existing buildings, resulting in energy and non-energy benefits. Quantifying the benefits of commissioning is challenging, but a 2009 study of 643 commercial buildings provided a solid initial data set to which we added 839 additional buildings for a significantly expanded and updated meta-analysis representing 34.7 million square meters (373 million square feet) of floor area. Since 2009 the commissioning industry has continued to grow, driven by building codes, utility programs, and rising awareness of commissioning benefits. In parallel, building controls have become more sophisticated, and analytics software has emerged to assist with commissioning. We find that delivery mechanism and market segment are key determinants of outcomes, although significant and cost-effective savings are found across the spectrum. Median primary energy savings for Cx projects in existing buildings ranged from 5 percent for those conducted under utility programs, 9 percent for monitoring-based commissioning utility programs (i.e., augmented with submetering and diagnostics), and 14 percent for Cx projects outside of utility programs. Across all project types, median savings ranged from 3 percent for the lodging market segment to 16 percent for public order and safety facilities. Outcomes did not vary significantly by building size or by market segment. Energy savings are rarely estimated for new construction commissioning. We found that the median costs of Cx were lower for the 2018 sample than for the 2009 sample—$\$$2.85 per square meter ($\$$0.26 per square foot) for existing buildings (a 33 percent reduction) and $\$$8.78 per square meter ($\$$0.82 per square foot) for new construction (a reduction of almost 50 percent). The median simple payback time for existing buildings was 1.7 years, with a 25th–75th percentile range of 0.8–3.5 years. Overall, this article summarizes these and other key findings, and discusses how the 2018 data reflects shifts in commissioning practice and outcomes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

MemFriend: Understanding Memory Performance with Spatial-Temporal Affinity

In HPC applications, memory access behavior is one of the main factors affecting performance. Improving an application’s memory access behavior involves optimizing data layout and/or restructuring code, and requires studying spatial-temporal data locality. Existing data locality analyses focus on single-location metrics and are restricted to evaluating temporal locality. We introduce spatial-temporal affinity metrics that quantify temporal access proximity, forward access correlation, and nearby access correlation between pairs of memory locations. We describe methods for distinguishing between potential vs. realized affinity and for reasoning about affinity at multiple resolutions (3D, 2D, 1D). Finally, we construct spatial-temporal affinity signatures that classify memory behavior and that be used to reason about changes in software (data relayout, code refactoring) or hardware (caching, prefetching). We describe methods for signature visualization, interpretation, and quantitative comparison of signatures. We evaluate our methodology using applications with variants that contrast data structures, data layouts and algorithms. We show that spatial-temporal affinity analysis provides novel insights and enables predictive reasoning about application performance when contrasted with reuse distance analysis.

Suriyakumar, Yasodhadevi↗

DOE OSTI2025

The ICEBERG Test Stand for DUNE Cold Electronics Development

ICEBERG is a liquid argon time projection chamber at Fermilab for the purpose of testing detector components and software for the Deep Underground Neutrino Experiment (DUNE). The detector features a 1.15m x 1m anode plane following the specifications of the DUNE horizontal drift far detector and a newly installed X-ARAPUCA photodetector. The status of ICEBERG is reported along with analysis of noise, pulser, and cosmic ray data from the ninth run beginning May 2024 with the goal of advising the DUNE collaboration on the optimal wire readout electronics configuration. In addition, development of an absolute energy scale calibration method is currently underway using known sources such as cosmic ray muon Michel electrons at the ~10 MeV scale and $^{39}$Ar decay electrons at the ~100keV scale. Research into AI-based identification of such events at the data acquisition level is introduced.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

FEbeam: Cavity and electron emission data conversion, processing, and analysis. A freeware toolkit for rf injectors

FEbeam is an all-in-one field emission data processing interface with the capability to analyze the field emission cathode performance in an rf injector by extracting the field enhancement factor, local field, and effective emission area from the Fowler–Nordheim equations. It also has the capability of processing beam imaging micrographs using its sister software, FEpic. Furthermore, the current version of FEbeam was designed for the Argonne Cathode Test-stand of the Argonne Wakefield Accelerator facility switch yard. With slight modifications, FEbeam could work for many rf field emission injectors. This software is open-source and can be found at GitHub.

43 PARTICLE ACCELERATORS↗

DOE OSTI2023

Life cycle analysis of a hydrogen production system based on solid oxide electrolysis cells integrated with different energy and wastewater sources

Hydrogen production via water electrolysis is a promising and evolving technology. The solid oxide electrolysis cell (SOEC) is one of the several technologies for this purpose. They are alternatives to the traditional hydrogen production from fossil fuels to enhance global energy decarbonization. However, in the bid for sustainability and a green economy, these technologies are not free from causing some environmental burdens. Using life cycle assessment (LCA), the greenhouse gas emission and degree of environmental impacts by these technologies can be identified and measured throughout their lifespan. This study addresses how to quantify these CO 2 emission impacts for an electrolytic system with different energy sources. The LCA of a novel integrated hydrogen production SOEC system with energy from solar photovoltaic and bituminous powerplant is performed using simaPro, the leading global LCA solution software. Measuring the environmental impact of the electrolytic operation in terms of weight, the bituminous powerplant poses damage which is, on average 700% more than solar PV. The thermal-to-hydrogen efficiency of the SOEC system is 56%, and a probable 28% reduction in carbon footprint with heat integration. The steam generation and the manufacturing of the SOEC have a very high environmental impact potential on the system. Here, we recommend LCA and net energy analysis is carried out for every new hydrogen technology and adequate comparison to enhance sustainable and green economy.

08 HYDROGEN↗

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 OSTI2026

Field and Model Data Associated with the Manuscript “Drivers of Streamflow Intermittency in Humid Regions: 2. Evaluating Controls on Flow Persistence in an Urbanized Catchment”

This package contains field data, modeling files, and scripts supporting the investigation of the drivers of streamflow intermittency in an urbanized catchment. It includes the field data collected from electrical resistivity tomography (ERT) surveys, distributed temperature sensing (DTS), continuous self-potential (SP) monitoring, groundwater and stilling well. In addition, it contains the data and results of the coupled water- and electrical-flow model developed using the COMSOL Multiphysics and Advanced Terrestrial Simulator (ATS), as well as software files and Jupyter notebooks used to process the data and generate figures in the manuscript submitted for peer review. The data archive is organized in the following directories: 1) Climate Includes hourly precipitation and daily evapotranspiration time series (2024 – 2025) provided as CSV files, alongside a text file detailing dataset units. 2) Coupled_model Field_Application subfolder contains the ATS XML input scripts, data files, output data for the SP site. It also contains the Jupyter notebook (Plot_final_calib.ipynb) to visualize the results of the modeled SP, stream-groundwater exchange and moisture content. The flow model simulation is executed using the ATS XML scripts and the included Python script (generate_data_set.py) to convert ATS output to COMSOL-ready input. COMSOL Multiphysics template (.m can only be used with COMSOL with MATLAB) is executed using the ATS output data to simulate the potential field. 3) Discharge Includes the electrical conductivity (EC) time series (provided as CSV files) from salt slug injections. It also includes the Jupyter notebook (Discharge_process.ipynyb) used to estimate discharge. All discharge measurements collated into rating_curve_processed.csv 4) DTS Contains collated DTS data including raw Stokes and anti-Stokes measurement (provided as .h5 file). It also includes DTS processing.ipynb, a Jupyter notebook for calibrating the DTS data using dts_calibration Python package. cooler_calibration.csv is the DTS calibration CSV used in the calibration sequence. 5) ERT Contains raw resistivity data (provided as CSV files), spatial location of each of the electrodes (provided as CSV files), and files used for the resistivity inversion. 6) Slug_test Includes the slug test data at all the groundwater wells provided as CSV files, as well as the Jupyter notebook (Slug_test.ipynb) for calculating hydraulic conductivity. 7) SP Contains the SP data collected in field at the SP sites (provided as CSV files). 8) Well_data Contains two subfolders: 1) Raw, which provides unprocessed pressure, electrical conductivity and temperature timeseries downloaded from the loggers in all the groundwater and stilling wells, and 2) Processed, which contains sorted, QA/QC timeseries data for each well. The data archive also contains data_process.ipynb, a Jupyter notebook used for field data analysis and generating figures (plotting well, SP, climate, and discharge data, as well as calculating head gradient at sites with nested groundwater wells). Note: Code files (.ipynb, .py, .xml) can be opened in any standard code editor, .exo file can be viewed using Paraview, .h5 files can be opened using HDFView software and h5py Python package, and .resipy file can be opened with the open-source ResIPy software.

ATS↗

DOE OSTI2021

Analysis of Spectral Lines in Large Databases of Synthetic Spectra for Massive Stars

In this paper, we describe a program that identifies in the optical spectrum the main parameters of a spectral line, namely the initial and final wavelengths, and the line depth. Moreover, using numerical calculations, it identifies and removes adjacent lines. Next, the program calculates the equivalent width and the FWHM. The software was tested in a sample of 300 lines in two databases of synthetic spectra generated by the CMFGEN and PoWR codes, and 300 lines in observed spectra from the IACOB database, showing a Gaussian distribution of relative errors, from which it is inferred that 80% of the measured lines have errors less than 17% and only 5% of the lines have errors greater than 26%. The program was also run on the entire database of 45,000 CMFGEN and 202 POWR synthetic spectra, generating a library of H i, He i, and He ii lines necessary to feed the FITspec code for the derivation of stellar parameters: effective temperature, surface gravity, and luminosity.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Experimental measurements and mathematical modeling of cold plate for aviation thermal management

Herein, this study, which has been motivated by the recent applications of the cold plate device in aviation thermal management, reports on physics-based mathematical models derived from the conservation laws of mass, momentum, and energy, and empiricism-based models. One of the objectives of the present work is to report on an elaborate and successful experimental work carried out on an additively manufactured device for the purpose of rigorously validating the numerical predictions. The excellent agreement between the numerical predictions and measured performance provides much needed confidence in the implementation, in the software package, of the offset-strip fin passage correlations, as well as in the software implementation of user-defined wavy fin correlations for aerospace heat exchangers and cold plates operating with ram air at Reynolds numbers below 8000. The contributions of this work can also be found in the development of a new and accurate thermal-hydraulic analysis procedure, referred to in this paper as plate-fin analogy. Results from this procedure are compared with those from thermal resistance network. The comparative study in this paper of the bulk and discrete enthalpy flux method is also new, as is the relative assessment of four off-set strip fin thermal-hydraulic models.

42 ENGINEERING↗

DOE OSTI2025

CoverM: read alignment statistics for metagenomics

SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses "Mosdepth arrays" for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results. AVAILABILITY AND IMPLEMENTATION: CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.

Aroney, Samuel T N↗

DOE OSTI2021

Scaling pair count to next galaxy surveys

ABSTRACT Counting pairs of galaxies or stars according to their distance is at the core of real-space correlation analyses performed in astrophysics and cosmology. Upcoming galaxy surveys (LSST, Euclid) will measure properties of billions of galaxies challenging our ability to perform such counting in a minute-scale time relevant for the usage of simulations. The problem is only limited by efficient access to the data, hence belongs to the big data category. We use the popular Apache Spark framework to address it and design an efficient high-throughput algorithm to deal with hundreds of millions to billions of input data. To optimize it, we revisit the question of non-hierarchical sphere pixelization based on cube symmetries and develop a new one dubbed the ‘Similar Radius Sphere Pixelization’ (SARSPix) with very close to square pixels. It provides the most adapted indexing over the sphere for all distance-related computations. Using LSST-like fast simulations, we compute autocorrelation functions on tomographic bins containing between a hundred million to one billion data points. In each case, we achieve the construction of a standard pair-distance histogram in about 2 min, using a simple algorithm that is shown to scale, over a moderate number of nodes (16–64). This illustrates the potential of this new techniques in the field of astronomy where data access is becoming the main bottleneck. They can be easily adapted to other use-cases as nearest-neighbours search, catalogue cross-match or cluster finding. The software is publicly available from https://github.com/astrolabsoftware/SparkCorr.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

The Future of High Energy Physics Software and Computing (V2.1)

Software and Computing (S&C) are essential to all High Energy Physics (HEP) experiments and many theoretical studies. The size and complexity of S&C are now commensurate with that of experimental instruments, playing a critical role in experimental design, data acquisition/instrumental control, reconstruction, and analysis. Furthermore, S&C often plays a leading role in driving the precision of theoretical calculations and simulations. Within this central role in HEP, S&C has been immensely successful over the last decade. This report looks forward to the next decade and beyond, in the context of the 2021 Particle Physics Community Planning Exercise ("Snowmass") organized by the Division of Particles and Fields (DPF) of the American Physical Society.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Measurement of Plutonium Ratios for CRM 137A Recertification

This report documents the analytical methodologies used by the Chemical and Isotopics Mass Spectrometry (CIMS) Group at the US Department of Energy’s Oak Ridge National Laboratory (ORNL) for plutonium isotopic ratio characterizations on purified ~1 mg units prepared by Lawrence Livermore National Laboratory (LLNL) from a mother solution created from an existing 250 mg unit of certified reference material (CRM) 137. The analytical processes described are designed to maintain traceability of the final certified attributes and to eliminate sources of systematic bias for the measurements described. The measurands for certification are the plutonium isotope ratios: 238 Pu/ 239 Pu, 240 Pu/ 239 Pu, 241 Pu/ 239 Pu, and 242 Pu/ 239 Pu. The preparation and analytical process included the following activities: Preparation of reference materials to be used as calibrants to establish traceability to the SI unit of mass for the isotopic analyses and quality controls. For the plutonium isotopic analyses, CRM 128 (a CRM comprising equal atoms of 239 Pu and 242 Pu) was used as the primary calibrant; Each CRM 137A unit was reconstituted using dilute high-purity HNO3. From each, seven replicates were distributed for the isotopic characterizations by thermal ionization mass spectrometry (TIMS) using the total evaporation (TE) method for isotope ratio measurements and MC-ICP-MS using a dynamic peak hooping method for secondary isotope ratio measurements; Due to time delay in the analyses from the last purification of the original CRM 137 mother solution by LLNL, an aliquot of the three provided plutonium units was purified using Eichrom TEVA separation methods to remove americium in-growth and uranium impurities; Minimally corrected data were reported from each analysis using reporting templates provided by the New Brunswick Laboratory Program Office (NBL PO) for the specific methods used for isotopic measurements. In addition, a copy of the instrument exports, Excel templates for isotopic data corrections, and the uncertainty budgets completed with the GUM Workbench software package were submitted to NBL PO.

07 ISOTOPE AND RADIATION SOURCES↗