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At least 91 records · Page 5

poppler-science

The “Poppler-science” software is a fork of the existing open-source Poppler project (https://poppler.freedesktop.org/) for converting PDF files to text. Modifications to the Poppler source code include (a) per-glyph optical character recognition (for correcting the non-standard font glyph remapping that is common in the scientific literature), (b) inference of text markup for commonly used scientific formatting (like superscripts and subscripts), (c) table and figure recognition, and (d) improved ordering of text output for complex scientific manuscripts (e.g., multi-column text, figure and table captions, etc.).

Gans, Jason [Los Alamos National Laboratory]

Analyzing and Exploring Training Recipes for Large-Scale Transformer-Based Weather Prediction

Abstract The rapid rise of deep learning (DL) in numerical weather prediction (NWP) has led to a proliferation of models which forecast atmospheric variables with comparable or superior skill than traditional physics-based NWP. However, among these leading DL models, there is a wide variance in both the training settings and architecture used. Further, the lack of thorough ablation studies makes it hard to discern which components are most critical to success. In this work, we show that it is possible to attain high forecast skill even with relatively off-the-shelf architectures, simple training procedures, and moderate compute budgets. Specifically, we train a minimally modified Swin Transformer V2 (SwinV2) on ERA5 data and find that it attains superior skill in terms of mean-square errors of deterministic forecasts when compared against the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS). Almost all DL–NWP systems share a core set of hyperparameters and design decisions. To aid and expedite future DL–NWP research, we present an in-depth, systematic exploration of different loss functions, model sizes and depths, patch sizes, and multistep training objectives. We also examine the model performance with metrics beyond the typical accuracy (ACC) and RMSE and investigate how the performance scales with model size. Through our open-source code, scoring pipelines, and models, we share our findings on key aspects of the training pipeline. These ablations reduce the necessity for expensive hyperparameter tuning and lower the barrier to entry for future DL–NWP research. Significance Statement This study investigates the potential of using large-scale transformer-based models for weather prediction, showing that it is possible to achieve high forecast accuracy with simpler, off-the-shelf architectures. By training a minimally modified SwinV2 transformer on ERA5 data, we show that the model achieves competitive forecast skill in terms of mean-square error for key variables, outperforming the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS) at all lead times. Our findings suggest that effective training strategies, such as multistep fine-tuning and channel-weighted losses, significantly enhance the model’s performance. However, we also highlight that these improvements come with trade-offs in other areas, such as ensemble spread and high-frequency spatial detail. This work highlights the promise of deep learning in improving weather forecasts, which could lead to better preparedness and response to weather events, ultimately benefiting society by providing more reliable weather predictions.

Willard, Jared D. [Lawrence Berkeley National Labo

Refining HPCToolkit for application performance analysis at exascale

As part of the US Department of Energy’s Exascale Computing Project (ECP), Rice University has been refining its HPCToolkit performance tools to better support measurement and analysis of applications executing on exascale supercomputers. To efficiently collect performance measurements of GPU-accelerated applications, HPCToolkit employs novel non-blocking data structures to communicate performance measurements between tool threads and application threads. To attribute performance information in detail to source lines, loop nests, and inlined call chains, HPCToolkit performs parallel analysis of large CPU and GPU binaries involved in the execution of an exascale application to rapidly recover mappings between machine instructions and source code. To analyze terabytes of performance measurements gathered during executions at exascale, HPCToolkit employs distributed-memory parallelism, multithreading, sparse data structures, and out-of-core streaming analysis algorithms. To support interactive exploration of profiles up to terabytes in size, HPCToolkit’s hpcviewer graphical user interface uses out-of-core methods to visualize performance data. The result of these efforts is that HPCToolkit now supports collection, analysis, and presentation of profiles and traces of GPU-accelerated applications at exascale. These improvements have enabled HPCToolkit to efficiently measure, analyze and explore terabytes of performance data for executions using as many as 64K MPI ranks and 64K GPU tiles on ORNL’s Frontier supercomputer. HPCToolkit’s support for measurement and analysis of GPU-accelerated applications has been employed to study a collection of open-science applications developed as part of ECP. This paper reports on these experiences, which provided insight into opportunities for tuning applications, strengths and weaknesses of HPCToolkit itself, as well as unexpected behaviors in executions at exascale.

Adhianto, Laksono

Observation of spin‑wave altermagnetic splitting in MnF2

-Contents of the Data Repository: - Polarized neutron diffraction data acquired in the (HK0) scattering plane. - Inelastic neutron scattering (INS) data from both unpolarized and polarized measurements with an incident neutron energy of Ei =9 meV.- - Reduced multidimensional single-crystal datasets (MDE) and corresponding S(Q,ω) slices used to generate all figures presented in the manuscript. - Julia source code and supporting input files used for spin-wave calculations, model fitting, and simulation of neutron scattering intensity maps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND

A tutorial review of machine learning-based model predictive control methods

Abstract This tutorial review provides a comprehensive overview of machine learning (ML)-based model predictive control (MPC) methods, covering both theoretical and practical aspects. It provides a theoretical analysis of closed-loop stability based on the generalization error of ML models and addresses practical challenges such as data scarcity, data quality, the curse of dimensionality, model uncertainty, computational efficiency, and safety from both modeling and control perspectives. The application of these methods is demonstrated using a nonlinear chemical process example, with open-source code available on GitHub. The paper concludes with a discussion on future research directions in ML-based MPC.

Wu, Zhe [Department of Chemical and Biomolecular E

Modularization of EDGE Workflows Using Nextflow: Improving the Efficiency and Maintainability of Bioinformatics Software

EDGE is a bioinformatics platform developed in 2016 by researchers at Los Alamos National Laboratory (LANL) to facilitate the analysis of next-generation sequencing data by researchers with varying levels of experience in bioinformatics (Li et al., 2017). Users with single-end, paired-end or long-read sequencing data can provide their reads as input to EDGE and select the combination of workflows to run that are most useful for their research (e.g., quality control of reads, genome assembly, or the taxonomic classification of input reads). Table 1 summarizes the modules available in EDGE. EDGE is available as a web platform at https://edgebioinformatics.org, as installable source code maintained on GitHub under a GPLv3 license, and as a publicly hosted Docker image.

59 BASIC BIOLOGICAL SCIENCES

Docker Containers for MCNP ® Development

Containers are a revolutionary technology in software development and deployment that provides a lightweight, portable environment for ensuring consistency across multiple computing environments. In anticipation of the MCNP 6.3.1 release, two Docker container images have been released on DockerHub for general use. The MCNP source code is not included in the images, and users are still required to obtain it through RSICC. The images produced by Docker are compliant with the OCI (Open Container Initiative) standards, ensuring compatibility with other container engines such as Podman or Kubernetes’ CRI-O. Initially, the images are stored under the author’s personal space on DockerHub (docker.io/azukaitis), but they will be relocated to a dedicated MCNP group space once approved. In the future, they will also be available through the registry feature of the https://github.com/lanl/mcnp-containers project. The use of Docker provides a pre-configured environment for building and running MCNP, ensuring reproducibility of results across various host architectures. This significantly improves consistency when running MCNP on different systems. Notably, executables and installers from the Docker images have successfully passed the MCNP development branch testing suite on x86-64 architectures, including Windows, macOS, and Linux operating systems. Furthermore, testing has demonstrated compatibility with macOS Docker in emulation mode on the latest Apple Mac M2 Ultra hardware, ensuring robust support even on the latest platforms. In this document, we will provide a step-by-step guide to using the Docker images across multiple platforms. Additionally, we will present performance numbers for building and running the MCNP test suite.

97 MATHEMATICS AND COMPUTING

A Roadmap for a Lightning Modeling Grand Challenge

This document is a roadmap for building an interconnected model of the physical processes that produce a lightning discharge, and its observable optical and radio signals. We call this a Lightning Modeling Grand Challenge, recognizing that significant effort and coordination of human and financial resources is required to realize the capability. The roadmap serves to outline the coordination of resources necessary to enable stitching together existing knowledge and model components to make a lightning prediction, and to test these predictions with observations. Such a capability does not currently exist. The roadmap is motivated not only by a spirit of scientific inquiry, but by practical challenges faced by US Federal and societal stakeholders. Advancements in lightning observations have outpaced our tests of integrated understanding, leaving many stakeholders unsure how to design their missions to properly detect and discriminate lightning, and unsure how to apply the sometimes-disagreeing lightning signals from diverse instruments. The time is right to connect existing theories and models to support stakeholders in understanding the signals they observe, for needs as diverse as climate monitoring, national security, weather forecasting, public safety, and protection of natural and built environments. The roadmap’s two main technical sections describe the components of a linked physical model, followed by a description of models of lightning signals and sensors that are driven by outputs from the physical model. The goal is to predict the time-varying physical properties of lightning that are self-consistent with the thunderstorm’s structure and dynamics. These lightning signals then propagate through the storm, with realistic dispersion and attenuation, to receivers on the ground or in space. At a high level, the model begins with weather (cloud) model output, including explicit prediction of the electrification of cloud particles. The cloud’s electrical structure drives a model of lightning physics, from initiation, through channel development, and discharges along those channels. Key lightning parameters, such as the temperature and currents in the channel, and their space and time distribution, are then used to produce optical and electromagnetic signal sources that propagate to modeled receivers. This architecture therefore generates a dataset suitable for comparison to existing and envisioned observing systems. The need for additional measurements and field campaigns to support model development is described. In each model sub-component, inputs, outputs, uncertainties, evaluation methods, and next steps are summarized, interleaved with references to the scientific literature. Identifying boundaries between the model sub-components aids in segmenting an integrated, complex model into practical work packages and system sub-components, allowing a diverse team to contribute and maintain the system. We estimate that at least five years of effort and a $\$$10M initial investment is necessary to make a significant step forward. Mechanisms to facilitate community coordination, including annual workshops and open-source code repositories, are described.

54 ENVIRONMENTAL SCIENCES

New model for the ion collection by cylindrical probes over a wide range of collisionality

Langmuir probes remain one of the most important diagnostic tools for plasma processing applications. Modern probe analysis usually relies on the electron current part of the Langmuir probe characteristic using the Druyvesteyn method. However, for electronegative plasmas or for discharges containing dust the analysis of the ion current attracted by the probe can be desirable to determine the ion density. But, even at low pressures of a few Pa, the ion current is affected by collisions due to the large cross section for charge exchange. Available theories for collisional or collision-enhanced ion currents onto probes are complex and not well validated. Thus, in this contribution, we compare available collisional probe theories for the ion current to results of particle-in-cell (PIC) simulations. To this end, the probe surrounded by a semi-infinite plasma is simulated using a modified version of the open-source code EDIPIC. A dataset of currents for different neutral gas pressures is obtained and compared to the different theories from the literature. Based on these results, we propose a simpler and more intuitive model for the ion current collected by the probe, based on the model of Gatti and Kortshagen (Phys. Rev. E 78, 046402, 2008), developed for the charging of dust particles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Computational Prediction of Infrasound Arrival Times and Directions from Stationary and Moving Impulsive Sources

This report addresses the need to predict infrasound signal arrival times and back azimuths at monitoring stations, enabling more focused and efficient searches within recorded waveform data. The primary challenge is estimating expected signal arrival windows for stationary and moving acoustic sources, such as chemical explosions, volcanic eruptions, meteoroids, and spacecraft re-entry events. To address this challenge, a reproducible methodology is described that uses simplified propagation speeds for boundary layer, tropospheric, stratospheric, and thermospheric atmospheric waveguides. While the Python source code itself is not freely available, this document provides detailed, step-by-step instructions, and equations enabling users to replicate and adapt the method independently. The method reliably predicts signal arrival intervals and back azimuths, thereby supporting rapid detection and accurate interpretation of infrasound events. Results demonstrate that this method effectively identifies plausible signal arrival intervals and directions, facilitating faster event detection and more reliable interpretation. This methodology directly supports atmospheric monitoring, planetary defense, and forensic analysis of explosive atmospheric events.

47 OTHER INSTRUMENTATION

OEDI—Solar Grid Integration Data and Analytics Library

As a part of the Open Energy Data Initiative, this effort aims to develop and demonstrate novel distribution state estimation, control optimization, and transient analysis as well as provide access to data, data integration, and mapping information. More specifically, the focus of the effort will be on physics-based distribution system state estimation, hybrid (physics-based and machine learning) distribution optimal power flow, and event detection/analysis for solar integration and analytics. This work will enable reproducible, robust, replicable, and generalizable R&D in simulation and emulation of solar system integration. These test models and datasets will provide an integrated library for developing and testing power system operation technologies. To make the library user-friendly, this project will provide data curation tools such as data translators, mapping scripts and APIs, database schemas and metadata, interfaces and user dashboard, source code for the reference algorithms, description of the use-cases/scenarios, and comprehensive information on all the assumptions.

14 SOLAR ENERGY

Resilience Through Data-Driven, Intelligent Designed Control: A Formal Methods Approach

The PNNL and GTRI team developed a strategy to integrate temporal logic rule specification for detection of cyber-intrusion in the source code and control algorithms of CPS using advanced cyber-data. The GTRI team utilized its capabilities in rule synthesis and temporal logic specifications for software assurance and verification to detect and predict impact of cyber-intrusions and malware in the computational and control algorithms of cyber-physical systems. The team also developed a testing and verification approach that could be used to validate the suggested approach against a realistic use-case CPS showcasing improvements in system impact prediction performance. Temporal logic offers a compact expression of events in absolute and relative time and has a formalized translation to state machines. As such, temporal logic rules can feasibly be synthesized to any system as a rule engine, with the process being formally verified to be correct. The goal here is to utilize temporal logic rules to detect cyber-attacks and manipulations in the computational algorithms and provide real-time software assurance and verification guarantees.

97 MATHEMATICS AND COMPUTING

Numerical Investigation of Fluid Flow and Space Charge in Liquid Argon Time Projection Chamber (LArTPC) Detectors

Overview This project focused on developing a high-fidelity numerical framework to simulate the multiphysics environment within Liquid Argon Time Projection Chamber (LArTPC) detectors. The primary objective was to characterize the complex interplay between ion transport, background fluid dynamics, and electric field distortions—a critical factor for the calibration and sensitivity of next-generation High Energy Physics experiments, such as DUNE. Technical Achievements The research successfully yielded a hybrid numerical space-charge solver utilizing a Cell-Centered Finite Volume Method (FVM) for ion transport coupled with a Finite Element Method (FEM) for electric potential. Key accomplishments include: • Verification & Validation: The 3-D solver was rigorously verified against 1-D analytical solutions, demonstrating high numerical accuracy in predicting space-charge-induced field deviations. • Field Distortion Analysis: 3D simulations revealed that space charge effects introduce significant non-uniformities in the electric field. Critically, the research identified that background LAr flow velocities, when comparable to ion drift velocities, markedly exacerbate these distortions. • Technology Transfer: The resulting source code and comprehensive user manuals were successfully transferred to collaborators at Fermilab, providing a portable computational tool for the broader scientific community. Challenges and Future Directions While the space-charge solver achieved all performance metrics, the integrated fluid dynamics modeling encountered convergence challenges stemming from the extreme 200-fold disparity in length scales between the detector's 37 mm inlet pipes and the 8-meter global domain. To address this, the project has identified a clear technical pivot toward Hierarchical Geometric Adaptive Mesh Refinement (HG-AMR). By implementing an h-type refinement strategy with hanging nodes, future iterations of this solver will be capable of resolving localized high-gradient inlet flows without the prohibitive computational costs of regular grids. This advancement, combined with data-driven uncertainty quantification based on MicroBooNE-style calibration, will enable the precise modeling of detector responses in large-scale cryogenic environments where direct measurement remains difficult. Impact The computational tools developed under this award provide a foundation for enhancing the energy resolution and spatial reconstruction of noble liquid detectors. By bridging the gap between theoretical fluid dynamics and experimental field calibration, this work supports the DOE’s mission to advance the frontiers of neutrino physics and dark matter detection.

42 ENGINEERING

C-HER Metadata Overview: Approach, Standards, and Rigor for the Centralized Health and Exposomic Resource

The Centralized Health and Exposomic Resource (C-HER) unifies environmental, demographic, geographic, and health-related data for exposomic research. The source data differ in format, geographic coverage, time period, resolution, terminology, and documentation. We use a common metadata framework to describe those differences and to record how each data resource has been processed, documented, and ingested. This document relates only to the C-HER metadata framework. It explains the information that is recorded for each resource, the standards used to organize that information, the conditions for metadata completeness, and the relationship between metadata and quality review. It is intended for those who need to understand what C-HER metadata communicates and how it supports appropriate use of the data. It is not an implementation specification or procedure. It does not document the database schema, source code, deployment configuration, transformation algorithms, or dataset-specific QA/QC thresholds. Those materials are maintained separately.

MacFarland, Midgie [ORNL] (ORCID:0009000807354078)

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

BLOC Site - ASSIST Thermodynamic Retrievals TROPoe v0.18 / Derived Data

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). This is a post-processed dataset and recommended for use. The profiles are retrieved every 10 minutes from instantaneous radiances observed with an Atmospheric Sounder Spectrometer by Infrared Spectral Technology (ASSIST, Michaud-Belleau et al. 2025) operated by NOAA Physical Sciences Laboratory (PSL) on Block Island for WFIP3. The spectral bands used in the retrieval are in the wavenumber range from 612 - 905.4 cm-1 and are specified in Turner and Löhnert (2021). Additional input data in TROPoe are cloud base height from a collocated ceilometer operated by NOAA GML and temperature, water vapor mixing ratio, and pressure from a collocated surface tower operated by NOAA PSL. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Upton, NY. The TROPoe docker container (version 0.18) is available from Docker Hub at https://hub.docker.com/r/davidturner53/tropoe/tags, and the source code code is available in the GitHub repository https://github.com/OAR-atmospheric-observations/TROPoe.

17 WIND ENERGY

NANT Site - ASSIST Thermodynamic Retrievals TROPoe v0.18 / Derived Data

This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). This is a post-processed dataset and recommended for use. The profiles are retrieved every 10 minutes from instantaneous radiances observed with an Atmospheric Sounder Spectrometer by Infrared Spectral Technology (ASSIST, Michaud-Belleau et al. 2025) operated by NOAA Physical Sciences Laboratory (PSL) on Nantucket Island for WFIP3. The spectral bands used in the retrieval are in the wavenumber range from 612 - 905.4 cm-1 and are specified in Turner and Löhnert (2021). Additional input data in TROPoe are cloud base height from a collocated ceilometer operated by NOAA GML and temperature, water vapor mixing ratio, and pressure from a collocated surface tower operated by NOAA PSL. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Upton, NY. The TROPoe docker container (version 0.18) is available from Docker Hub at https://hub.docker.com/r/davidturner53/tropoe/tags, and the source code code is available in the GitHub repository https://github.com/OAR-atmospheric-observations/TROPoe.

17 WIND ENERGY