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At least 811 records · Page 45

VISION: a modular AI assistant for natural human-instrument interaction at scientific user facilities

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an x-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instruments and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex—a synthetic extension to the cognition of scientists—may radically transform scientific practice and discovery.

36 MATERIALS SCIENCE↗

LinkML: an open data modeling framework

Background Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, nonstandardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. Findings LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. Conclusions LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at their origin. LinkML documentation and code are available at https://linkml.io/.

AI-ready data↗

Code Artifact for: Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data [SWR-21-96]

This repository contains data ingestion, feature extraction, and analysis code used in NREL Technical report "Clustering Analysis of Commercial Vehicles Using Automatically Extracted Features from Time Series Data." The code is written in Python. The ETL and feature extraction code must be run in a Spark context. The analysis code can be run without Spark, provided you have pre-computed features in a CSV file. Analysis code related to the NREL Technical Report NREL/TP-2C00-74212. Includes PySpark functions to perform trip segmentation and feature extraction over big time series data in Apache Spark. Includes "domain specific" features such as Aerodynamic Speed (ft/s), Characteristic Acceleration (ft/s2), Percent Below 55 (%), Percent Zero (%), Stops Per Mile, Average Speed (mph), Maximum Speed (mph), and Speed Standard Deviation (mph). Includes Pyspark UDF to compute "domain agnostic" features using the TSFresh library. This software record also includes the analysis notebooks and code to generate the results in the previously mentioned technical report.

Perr-Sauer, Jordan↗

materialsCloudCompute

materialsCloudCompute (mCC) is a software package for running easily parallelizable materials science theoretical computations on Amazon Web Services (AWS) infrastructure. mCC provides tools to partition out computational problem into smaller subproblems which can be run in parallel, and ensure that each of those subproblems completes successfully. It utilizes the following AWS services: EC2, S3, and RDS. It operates by launch a managing EC2 instance, which can launch worker instances that perform the calculations. The Managing instance tracks the subproblems and ensures that the Worker instances continue to operation, killing and relaunching them if they fail.

Forbes, David↗

DEPDOSE

DEPDOSE is an open-source computer application which combines the KDEP respiratory tract deposition software with committed equivalent dose coefficient tables from the DC_PAK internal dosimetry package. DEPDOSE allows the user to rapidly produce tables of dose coefficients to workers and members of the public inhaling a precisely defined, user-specified aerosols using the ICRP 60 series methodology. Combined with a plume dispersion modeling system such as QUIC, this makes it possible to predict radiation doses downstream from an accidental or intentional release of radioactive materials. For this work, a radioactive plume was calculated to members of the public downstream from a plausible release of radionuclides into the atmosphere.

Klumpp, John↗

MAPSTER

MAPSTER Observer is a light-weight software package that can be installed on field deployed computers which automatically manages data and creates metadata packages designed to organize large datasets, making them easy to retrieve and share.

Larson, MatthewD↗

Scribe Network API v.1.0.0

SAND2023-07864O Scribe Network API is an add-on tool for Scribe3D software. Scribe Network API documents tabletop exercises in trainings and plays back simulated videos of the scenarios and responses. Users can apply the software to compiled projects, or to a simple visual studio project solution package. The software runs a web application that relays information between computers using Scribe3D through a web application, or web app. The web app involves a representational state transfer (REST) application programming interface that handles sending and receiving Scribe save files and an SQL server that stores the save files. This follow-on package allows users to facilitate a networked tabletop exercise. 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.

Noel, Todd↗

via-wind (A Visual Impact Assessment Tool for Wind Turbines) [SWR-24-87]

Via-wind is an open-source tool for conducting visual impact assessments for wind turbines. It combines geographic information system (GIS) and 3D simulation methods to account for the key factors driving the visual impact of installed wind turbines, including distance, viewing angle, turbine orientation, visual exposure, and the cumulative effects of multiple turbines. This software is optimized for use in high-performance computing environments to enable large scale (e.g., country-wide) analysis, but can also be run on a single server or personal computer. For more information, please see the related journal article: https://www.sciencedirect.com/science/article/pii/S0306261924021846

Lopez, Anthony↗

Verification of EvaluateFLux Utility Program

The EvaluateFlux program is a post-processing utility program for DIF3D, specifically DIF3D-VARIANT which handles Cartesian and hexagonal geometries. The EvaluateFlux program was developed to allow users to obtain flux and power traverses through the geometry domain, and its initial purpose was to facilitate foil analysis by evaluating the flux solution from DIF3D-VARIANT and combining it with foil cross section data. The EvaluateFlux program can calculate the neutron flux, as well as the reaction rates, at any user provided evaluation point. It does this by identifying the spatial mesh associated with the evaluation point and then evaluates the polynomial based neutron flux moments stored in the NHFLUX file at that point. The output of EvaluateFlux varies depending on the input setup. The maximum output includes the neutron flux and microscopic and macroscopic reaction rates at each evaluation point. The purpose of this work is to verify the outputs of EvaluateFlux. Simple models that have hand calculatable results are first defined and used to verify the EvaluateFlux outputs. More complex cases are then added where a duplicate program of EvaluateFlux that uses PrintTables outputs of the binary files is used to verify the EvaluateFlux outputs. In those complex cases, hand calculations of selected evaluation points were also displayed to confirm the software verification. For all the tests done, the hand calculations agreed well with those calculated by EvaluateFlux. For the larger complex problems, the duplicate program that can process hundreds of evaluation points was able to identify that zero points within some meshes have large errors. This aspect was attributed to the truncation error on the input provided to the duplicate program and is not a concern for the accuracy of the EvaluateFlux software.

97 MATHEMATICS AND COMPUTING↗

Electron Beam Irradiation for Water Treatment of Per- and Polyfluoroalkyl Substances (PFAS)

Per- and polyfluoroalkyl substances (PFAS) are widely used but are now considered a water contamination risk. Fermi National Accelerator Laboratory’s IARC group has demonstrated that passing water through electron beam radiation can destroy PFAS. This project aims to develop a process to scale the system for bulk water treatment. The key is efficient radiation usage, ensuring that all water receives only the minimum dose. Software was developed for this purpose, consisting of a computational fluid dynamics model (CFD) in COMSOL, which calculates particle trajectories through the radiation area. A MATLAB script integrates the radiation dose of these particles, and statistical analysis is performed to evaluate the radiation utilization efficiency. These models are validated with a flow test where colored dye is injected and optically tracked. Radiation dose is measured by testing under an e-beam to measure the degradation of a PFAS analog.

Mueller, Scott [Northern Illinois U.]↗

Studying Performance Portability of LAMMPS across Diverse GPU-based Platforms

The molecular dynamics simulation software, LAMMPS, utilizes the Kokkos acceleration library to port computation to a diverse set of architectures including those based on GPU accelerators. In addition to Kokkos, LAMMPS contains a vast code base that leverages the CUDA application programming interface using library functions such as cuFFT, CUDA’s fast-fourier transform (FFT) library, and, more recently, also support for AMD’s Heterogeneous Interface for Portability (HIP) that is rapidly growing. While preparing LAMMPS tests for the AMD GPU-based test system precursors to Frontier, we investigated several strategies for accelerating LAMMPS on AMD GPUs, using the AMD Instinct MI100 and MI250X. In this work, we integrated the HIP FFT library, hipFFT, into the particle-particle particle-mesh (PPPM) long-range solver, which allowed the porting of PPPM calculations to the GPUs. Kokkos behavior on the MI100 and MI250X was also investigated through the package kokkos command of LAMMPS, targeting com- munication, memory usage, and particle grid decomposition. The Tersoff, Reax, Lennard-Jones (LJ), EAM, Granular, and PPPM potentials were investigated in this effort, and results from these experiments are provided. The selected potentials were run on Spock (AMD Instinct MI100), Crusher (AMD Instinct MI250X), AFW HPC11 (NVIDIA A100) and Summit (NVIDIA V100), for comparison. Operational roofline models were constructed and analyzed for the Tersoff, Reax, and Lennard-Jones potentials on Crusher and Summit.

Hagerty, Nick↗

Impacts of Modern IT on LCLS-II Experiment Control Systems

Modern information technology (IT) is a broad term with vague and somewhat arbitrary boundaries which can depend on any given novice or subject matter expert’s notional understanding. For the purposes of this article, IT can be understood as standards in communication, computational power, and storage. Additionally, impacts of modern IT extend beyond its products of hardware and software to include associated work practices and engineering processes.

97 MATHEMATICS AND COMPUTING↗

SAM Theory Manual

The System Analysis Module (SAM) is an advanced and modern system analysis tool under development at Argonne National Laboratory for advanced non-LWR reactor safety analysis. It aims to provide fast-running, modest-fidelity, whole-plant transient analyses capabilities, which are essential for fast turnaround design scoping and engineering analyses of advanced reactor concepts. While SAM is being developed as a system-level modeling and simulation tool, advanced modeling techniques being implemented include a reduced-order three-dimensional module, pseudo 3-D conjugate heat transfer modeling in reactor core, flexible and multi-scale modeling of heat transfer between fluid and structures, in addition to the advances in software environments and design, and numerical methods. SAM aims to be a generic system-level safety analysis tool for advanced non-LWRs, including Liquid-Metal-cooled fast Reactors (LMR), Molten Salt Reactors (MSR), Fluoride-salt-cooled High- temperature Reactors (FHR), and High-Temperature Gas-cooled Reactors (HTGR). SAM takes ad- vantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented computational framework (MOOSE), and its underlying meshing and finite-element library and linear and non-linear solvers, to leverage the modern advanced software environments and numerical methods. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As new code capabilities and features are added, the SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Machine Learning Based Software Package for Reproducible Data Analysis for Electron Microscopy

Advances in hardware and computation technologies are enabling large hyperspectral imaging during Electron Microscopy (EM), resulting in datasets being produced at rapidly increasing spatial and temporal resolutions. This presents exciting opportunities for microstructure analysis, but also poses great challenges in data analysis. Under this STTR program, QuesTek Innovations LLC, a leader in the field of integrated computational materials engineering (ICME), collaborated with Lawrence Livermore National Laboratory and Argonne National Laboratory. The team developed an open-source machine learning (ML) powered tool for EM data analysis of multiple systems and data types, and collected EM data for ML model development using the cutting-edge PicoProbe equipment at Argonne National Laboratory.

Lin, Yu↗

Verification of the PERSENT Software

Ongoing commercial design activities require a thorough verification of the Argonne Reactor Computation codes to be performed. DIF3D is central to this system and substantial work has been done to verify its accuracy on several identified commercial needs. This manuscript details the verification work done on PERSENT which relies upon the DIF3D for its forward and adjoint flux solution.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Verification of the PERSENT Software

Ongoing commercial design activities require a thorough verification of the Argonne Reactor Computation codes be performed. DIF3D is central to this system and substantial work has been done to verify its accuracy on several identified commercial needs. This manuscript details the verification work done on PERSENT which relies upon the DIF3D code for its forward and adjoint flux solution. Previous work identified the PERSENT features required to be verified to support commercial design activities, features of which are generally applicable to hexagonal-Z fast reactor designs. The scope of this verification effort includes verifying PERSENT’s ability to correctly calculate four key quantities: perturbation worth distributions, kinetics parameters, sensitivity coefficients, and cross section uncertainty quantification. This manuscript provides the verification tasks and their results with respect to these quantities needed for commercial design activities. For the perturbation worth distributions, hand calculations are deployed to verify the PERSENT calculated results. Similarly, hand calculation of the PERSENT computed kinetics parameters is also used to verify the PERSENT results. In both of these, the input to PERSENT is manipulated to ensure the hand calculation exactly matches the equations PERSENT is calculating. The sensitivity coefficients involve calculating the derivatives of a parameter (such as reactivity worth), with respect to the cross section data. Direct finite difference calculations with DIF3D are used to verify the PERSENT calculated results. For the uncertainty quantification, manufactured input to PERSENT is used to allow an exact hand calculation to reproduce the PERSENT calculated results. The work detailed in this report verified that significant issues were identified for earlier versions of PERSENT for sensitivity coefficients which were corrected in this work and thus version 12.1.0 of PERSENT must be used to reproduce all of the verified work in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamComboDMLinear

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs.

97 MATHEMATICS AND COMPUTING↗

MFC 5.0: An exascale many-physics flow solver

Many problems of interest in engineering, medicine, and the fundamental sciences rely on high-fidelity flow simulation, making performant computational fluid dynamics solvers a mainstay of the open-source software community. Previous work MFC 3.0 was made a published, documented, and open-source solver via Bryngelson et al. Comp. Phys. Comm. (2021) with numerous physical features, numerical methods, and scalable infrastructure. MFC 5.0 is a significant update to MFC 3.0, featuring a broad set of well-established and novel physical models and numerical methods, as well as the introduction of GPU and APU (or superchip) acceleration. Here, we exhibit state-of-the-art performance and ideal scaling on the first two exascale supercomputers, OLCF Frontier and LLNL El Capitan. Combined with MFC’s single-accelerator performance, MFC achieves exascale computation in practice, and achieved the largest-to-date public CFD simulation at 200 trillion grid points as a 2025 ACM Gordon Bell Prize finalist. New physical features include the immersed boundary method, N-fluid phase change, Euler–Euler and Euler–Lagrange sub-grid bubble models, fluid-structure interaction, hypo- and hyper-elastic materials, chemically reacting flow, two-material surface tension, magnetohydrodynamics (MHD), and more. Numerical techniques now represent the current state-of-the-art, including general relaxation characteristic boundary conditions, WENO variants, Strang splitting for stiff sub-grid flow features, and low Mach number treatments. Weak scaling to tens of thousands of GPUs on OLCF Summit and Frontier and LLNL El Capitan achieves efficiencies within 5% of ideal to over 90% of their respective system sizes. Strong scaling results for a 16-times increase in device count show parallel efficiencies over 90% on OLCF Frontier. MFC’s software stack has undergone further improvements, including continuous integration, which ensures code resilience and correctness through over 300 regression tests; metaprogramming, which reduces code length while maintaining performance portability; and code generation for computing chemical reactions

Computational fluid dynamics↗