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At least 379 records · Page 21

Cross-facility science with the Superfacility Project at LBNL

As data sets from DOE user science facilities grow in both size and complexity there is an urgent need for new capabilities to transfer, analyze and manage the data underlying scientific discoveries. LBNL's Superfacility project brings together experimental and observational research instruments with computational and network facilities at the National Energy Research Scientific Computing Center (NERSC) and the Energy Sciences Network (ESnet) with the goal of enabling user science. Here, we report on recent innovations in the Superfacility project, including advanced data management, API-based automation, real-Time interactive user interfaces, and supported infrastructure for 'edge' services.

Enders, B↗

MCNP6 Source Primer: Release 1.0

This document contains examples of MCNP general source usage to support the MCNP6 User’s Manual. The examples range from basic to advanced sources with different applications. There are also examples of how MCNP can fail and warnings for the users to look for at the output to ensure proper results are being created. The overall aim of this document is to provide solid examples of how to define sources with MCNP as well as how to verify the sources are setup properly. The reasoning for needing such complex sources is not discussed in the present work. Also, this document is not meant to be exhaustive of every MCNP source option and combinations of source options possible. However, it is intended to frequently update this document with new source examples provided by users. Please feel free to contact the MCNP6 development team to learn about how to submit a new or updated source example. Please include “General Sources Primer” in the subject line to route the request to the appropriate developers.

97 MATHEMATICS AND COMPUTING↗

Seer: Using Mochi for In Situ Analysis

Seer is an in situ framework that allows steering of in situ analysis. Seer works with other existing in situ software such as ParaView Catalyst. It supports multi-user analysis

97 MATHEMATICS AND COMPUTING↗

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↗

Basic Research Needs in The Science of Scientific Software Development and Use: Investment in Software is Investment in Science

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 are 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. Increased investment, especially in the characterization and improvement of how scientific software is developed and used, is important for sustaining and improving the impact of software as the scope and complexity of scientific efforts expand. Without this investment, we face the risk of diminishing returns on our software investments because the demands for increased functionality, usability, reliability, and more will not be sufficiently met. 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. For many years, DOE/SC software investments have provided tremendous value to the scientific community. We want to continue and further improve the value of DOE/SC software efforts by using a scientific approach to understanding and improving how scientific software is developed and used. 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, which built on insights from 124 pre-workshop position papers, 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, impacting discoveries, policy, and technological development. To maintain and improve confidence in science delivered via software, we must improve the processes and tools that help us create and use software, and this enhancement requires a deep understanding of the diverse array of teams and individuals doing the work.

97 MATHEMATICS AND COMPUTING↗

Applying the Risk Management Framework: The Distributed Energy Resource Risk Manager

As part of a multiyear effort, the National Renewable Energy Laboratory (NREL) has dedicated resources to understand and identify cybersecurity weaknesses in distributed energy resources (DERs) by performing assessments. Due to a lack of standardization and rapidly increasing adoption of DERs, there is a critical need to address cybersecurity needs for DER systems in an interactive way. Furthermore, federal agencies, which are required to obtain an authority to operate, are challenged by the complexities of including their DERs. To help meet this need, in early 2020, NREL released the Distributed Energy Resources Cybersecurity Framework (DERCF) and accompanying Web application. This process is supported by the Risk Management Framework (RMF) developed by the National Institute of Standards and Technology. This project, referred to as the DERCF RMF application, expands on the existing DERCF work to include methods that support walking a user through the seven RMF steps. The tool will be available for download at no cost from [link ]. The purpose of this paper is to describe the steps the DERCF team at NREL took to understand Steps 1-5 of the RMF process. Additionally, this document will identify future work on the first five steps as well as a plan for Steps 6 and 7.

24 POWER TRANSMISSION AND DISTRIBUTION↗

MTA Secondary Beamline Production and Optics Optimization

A new secondary beamline was recently installed in the MeV Test Area (MTA) with the objective of enhancing mu+/mu- production by factors of 3/8 by using a tungsten target versus the conventional graphite production target using the 400 MeV Fermilab proton Linac beam. Ultra-low energy muon beams can support world-class physics experiments for fundamental muon measurements, sensitive searches for symmetry violation, and precision tests of theory. Extensive production studies have confirmed higher muon yield from heavy targets (tungsten vs carbon), but also, surprisingly, showed significant differences in production fluence and energy spectrum between modern hadronic models (GENIEhad) and between GEANT and MCNP. Studies are also underway towards a high-efficiency source of muonium by stopping the mu+ beam in superfluid helium. Muon fluxes can be measured at MTA including using higher-Z and novel target geometries to test hadronic and production models which are critical to understanding ongoing experiments (Mu2e) and will significantly impact the planning of future HEP experiments and planning PIP II facilities. The MTA beamline will additionally support a broad user muon test beam for future experiments and R&D.

Ahmed, Shiza↗

Desert-Urban SysTem IntegratEd AtmospherIc Monsoon (DUSTIEAIM) in the Southwestern United States

Phoenix, Arizona, is the fifth-largest city in the United States with about 1.6 million residents. It is also considered to be the hottest major city in the country, having set a record of 31 consecutive days with temperatures above 110 F (43 C) in summer 2023. Phoenix depends on the Colorado River for over a third of its water supply, but there are questions about how much water will eventually be available to serve the rapidly growing metropolitan area, especially in such extreme heat. Current earth system models struggle to accurately capture precipitation in the Southwestern United States, especially in relation to the summertime North American Monsoon.

54 ENVIRONMENTAL SCIENCES↗

RAG for FLAG: AI Assistance for a Physics Code

Artificial intelligence (AI) has quickly become an important tool in scientific research, where significant efforts are underway to develop tools that will expedite the research process. One area of particular impact is scientific software, which can be particularly complex, and therefore time consuming to learn and use effectively. AI assistants are increasingly helping to streamline the process by performing tasks such as interactively answering user questions or suggesting solutions. Los Alamos National Laboratory (LANL) develops several advanced scientific codes, such as FLAG, which can be used to run multiphysics simulations. With this study, our goal was to develop an AI assistant for FLAG that could help make the process of understanding the software and running physics simulations more efficient. To develop an AI assistant for FLAG, we used a method called retrieval-augmented generation (RAG), which is a technique that uses information from relevant data sources to enhance the accuracy of large language models (LLMs). We used the FLAG user manual and other FLAG documentation as the knowledge base for the RAG system. When a user provides a query, RAG retrieves relevant sections from the knowledge base in response, then uses those excerpts to generate grounded and contextually rich answers. We found that our AI assistant was able to provide context aware answers and source references to user queries. To evaluate performance, we developed a set of 40 benchmark questions and compared the accuracy of the responses to those of two standard LLMs without retrieval. Our AI assistant significantly outperformed the standard LLMs at answering FLAG-related questions, with an 82.5% accuracy rate, compared to 47.5% for both of the standard LLMs. This has the potential to make the process of learning and using FLAG much easier, especially for new users. Ultimately, it supports LANL’s broader mission by empowering scientists and engineers to focus more on discovery and analysis rather than on navigating complex software systems.

97 MATHEMATICS AND COMPUTING↗

LANSCE Accelerator Modernization Project Conceptual Design Report

The accelerator complex now known as the Los Alamos Neutron Science Center (LANSCE) began operation in 1972 as LAMPF, the Los Alamos Meson Production Facility. In the intervening 53 years, the complex has been expanded in capability several times, both in terms of its accelerator performance and the user facilities it supports.

43 PARTICLE ACCELERATORS↗

National Hydropower Fish Passage Database User's Guide and Methodology

Fish passage facilities are used to mitigate the impacts of hydropower dams on migratory fish in rivers, but information on the location, types, and characteristics of this infrastructure is incomplete at a national scale. Researchers at Oak Ridge National Laboratory partnered with federal agency and industry stakeholders to create the first national-scale database of fish passage infrastructure at U.S. hydropower developments. This database contains information of great value to a broad range of stakeholders; it includes fish passage facility engineering characteristics, targeted fish species, operational schedules, and costs. This data resource addresses a large gap in knowledge of the deployment of fish passage technology and is freely available to members of the hydropower community, including federal and state regulators and resource agencies, non-governmental organizations, industry, and other user groups to support project planning and regulatory (re)licensing activities. This database supports the U.S. Department of Energy Water Power Technologies Office objective to develop decision support tools and data resources that improve environmental performance and ensure hydropower’s long-term value to the American public.

13 HYDRO ENERGY↗

ORNL National Hydropower Fish Passage Database

Fish passage facilities are used to mitigate impacts of hydropower dams to migratory fish in rivers, but information on the location, types, and characteristics of this infrastructure is incomplete at a national scale. Researchers at Oak Ridge National Laboratory (ORNL) partnered with fish passage engineers and hydropower experts from the US Fish and Wildlife Service (USFWS), the National Oceanic Atmospheric Administration’s National Marine Fisheries Service (NOAA NMFS), and the Low Impact Hydropower Institute (LIHI) to create the first national scale database of fish passage infrastructure at US hydropower developments. This database consists of the ORNL_Fish_Passage_Dataset.zip file with 13 individual .csv files that contain information on fish passage facility engineering characteristics, targeted fish species, operational schedule, and costs. which is of great value to a diverse range of stakeholders. This information was collected between December 2023 and July 2025 from project partners, other hydropower stakeholders, online datasets available for download, and a stakeholder questionnaire Information. This data resource addresses a large gap in knowledge of the deployment of fish passage technology and is freely available to members of the hydropower community, including federal and state regulators and resource agencies, non-governmental organizations (NGOs), industry, and other user groups to support project planning and regulatory (re)licensing activities. This database supports the US Department of Energy Water Power Technologies Office objective to develop decision support tools and data resources that improve environmental performance and ensure hydropower’s long-term value to the American public.

Matson, Paul [Oak Ridge National Laboratory (ORNL)↗

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗

Policy-Driven Sustainable Saline Drainage Disposal and Forage Production in the Western San Joaquin Valley of California

Environmental policies to address water quality impairments in the San Joaquin River of California have focused on the reduction of salinity and selenium-contaminated subsurface agricultural drainage loads from westside sources. On 31 December 2019, all of the agricultural drainage from a 44,000 ha subarea on the western side of the San Joaquin River basin was curtailed. This policy requires the on-site disposal of all of the agricultural drainage water in perpetuity, except during flooding events, when emergency drainage to the River is sanctioned. The reuse of this saline agricultural drainage water to irrigate forage crops, such as ‘Jose’ tall wheatgrass and alfalfa, in a 2428 ha reuse facility provides an economic return on this pollutant disposal option. Irrigation with brackish water requires careful management to prevent salt accumulation in the crop root zone, which can impact forage yields. The objective of this study was to optimize the sustainability of this reuse facility by maximizing the evaporation potential while achieving cost recovery. This was achieved by assessing the spatial and temporal distribution of the root zone salinity in selected fields of ‘Jose’ tall wheatgrass and alfalfa in the drainage reuse facility, some of which have been irrigated with brackish subsurface drainage water for over fifteen years. Electromagnetic soil surveys using an EM-38 instrument were used to measure the spatial variability of the salinity in the soil profile. The tall wheatgrass fields were irrigated with higher salinity water (1.2–9.3 dS m -1 ) compared to the fields of alfalfa (0.5–6.5 dS m -1 ). Correspondingly, the soil salinity in the tall wheatgrass fields was higher (12.5 dS m -1 –19.3 dS m -1 ) compared to the alfalfa fields (8.97 dS mm -1 –14.4 dS mm -1 ) for the years 2016 and 2017. Better leaching of salts was observed in the fields with a subsurface drainage system installed (13–1 and 13–2). The depth-averaged root zone salinity data sets are being used for the calibration of the transient hydro-salinity computer model CSUID-ID (a one-dimensional version of the Colorado State University Irrigation Drainage Model). This user-friendly decision support tool currently provides a useful framework for the data collection needed to make credible, field-scale salinity budgets. In time, it will provide guidance for appropriate leaching requirements and potential blending decisions for sustainable forage production. This paper shows the tie between environmental drainage policy and the role of local governance in the development of sustainable irrigation practices, and how well-directed collaborative field research can guide future resource management.

54 ENVIRONMENTAL SCIENCES↗

1000 Soils Pilot Dataset, version 8, May 2025

This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback. Data completed include: Geochemistry, texture, respiration, and enzyme activities FTICR-MS organic matter chemistry Microbial biomass C and N TOC/TDN of water-extractable OM X-ray computed tomography (derived metrics available here, raw data available upon request) Metagenomes; a variety of data formats are available upon request Soil hydraulic properties Data in progress: LC-MS/MS in development, timeline TBD, inquire for status 1000S_processed_BGC_summary.csv contains all available biogeochemical data; microbial biomass C and N; and TOC/TDN of water-extractable OM; and 1000S_Tomography.xslx contains a summary of data generated via X-ray computed tomography. icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Soil Hydraulics_corrected_02042025.xlsx contains soil hydraulics information. Readme File_v4.xlsx is the readme file. Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file and all raw data are available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs. For more information, please see: https://www.emsl.pnnl.gov/monet and https://sc-data.emsl.pnnl.gov/monet Acknowledgment: Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.

biogeochemistry↗

Warm boundary-layer cloud properties and cloud susceptibilities product at the ARM ENA observatory

Cloud liquid water path, albedo, and cloud fraction susceptibilities for marine warm boundary-layer clouds are quantified using the Meteosat retrieved cloud microphysical properties at the ARM Eastern North Atlantic (ENA) observatory in the Azores. The Meteosat cloud retrievals are based on the methods applied by the Clouds and the Earth’s Radiant Energy System (CERES) project, which are specifically tailored to support the ARM user facility over the ARM ground-based observation sites (enavisstpx2dm11minnisX1.c1). Cloud susceptibility is quantified as the slope between cloud properties and Nd within a 1-degree-by-1-degree grid box at each satellite time step using a least-square regression. To reduce uncertainties associated with the adiabatic assumption in the Nd retrieval, for each cloud object, we exclude cloudy pixels at the cloud edge, defined as those adjacent to cloud-free pixels. To minimize influence of cloud heterogeneity and co-variability on the retrieved cloud susceptibility, cloud properties are averaged to 0.25-degree resolution using the 3-km pixel-level retrieval, and the 1-degree cloud susceptibilities are estimated using the smoothed data. Cloud type classification is applied to distinct cloud object, labeling all contiguous cloudy pixels. Marine warm boundary-layer clouds are defined as clouds with 90% of cloud tops below 3km, and Meteosat retrieved cloud phase as liquid.

54 ENVIRONMENTAL SCIENCES↗

Sigma 2 Graphic Display Software Program Description

A general purpose, user oriented graphic support package was implemented. A comprehensive description of the two software components comprising this package is given: Display Librarian and Display Controller. These programs have been implemented in FORTRAN on the XDS Sigma 2 Computer Facility. This facility consists of an XDS Sigma 2 general purpose computer coupled to a Computek Display Terminal.

Johnson, B. T.↗