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At least 127 records · Page 7

Best practices in software development for robust and reproducible geoscientific models based on insights from the Global Carbon Budget's dynamic vegetation models

Computational models play an increasingly vital role in scientific research by enabling the numerical simulation of complex processes. Such models are also fundamental in geosciences. For instance, they offer critical insights into the impacts of global change on the Earth system today and in the future. Beyond their value as research tools, models are also software products and should therefore adhere to certain established software engineering standards. However, scientists are rarely trained as software developers, which can lead to potential deficiencies in software quality like unreadable, inefficient, or erroneous code. The complexity of models, coupled with their integration into broader workflows, also often makes it challenging to reproduce results, evaluate processes, and build upon them. In this paper, we review the state and current practices of the development processes of the state-of-the-art land surface models used by the Global Carbon Budget. We combine the experience of modelers from the respective research groups with the expertise of software engineers from tech companies to outline key principles and tools for improving software quality in research. We explore four main areas: (1) model testing and validation, (2) scientific, technical, and user documentation, (3) version control, continuous integration, and code review, and (4) the portability and reproducibility of workflows. Our review reveals that while modeling communities are incorporating many best practices, significant room for improvement remains in areas such as automated testing, automated documentation, and reproducibility. Therefore, we here identify and promote essential software engineering practices, including numerous examples of practices from within the community that can serve as guidelines for other models and could help streamline processes across the entire community. We conclude with an open-source example implementation of these principles, demonstrating portable and reproducible data flows, a continuous integration setup, and web-based visualizations. This example may serve as a practical resource for model developers, users, and all scientists engaged in scientific programming.

Gregor, Konstantin [Technical Univ. of Munich (Ger

Data Integration and Visualization for Enhanced Resilience and Sustainability in Hydropower (DIVERS-H)

U.S. hydropower plants face potential threats from shrinking water supply, rising demands, and warmer stream temperatures from various causes. Power plant owners, operators, and regulators require new tools to take advantage of and interpret the diverse range of scientific data being produced by both observational methods (for example, satellite, radar, stream gauges) and computer modeling methods that evaluate and predict how earth's dynamic systems (atmosphere, oceans, land surface, and sea ice) are changing and interacting. Combining datasets such as these with AI-based analyses introduces a novel decision support system to help users anticipate and address potential impacts on power generation stations. This new technology has been named DIVERS-H for "Data Integration and Visualization for Enhanced Resilience and Sustainability in Hydropower." In Phase I, technical feasibility was established with the development and demonstration of all the new technologies that are required. Most notably, DIVERS-H will use new artificial intelligence (AI) methods to capture the complex dynamics of water availability, demand, and environmental changes. In addition, new data management software was developed, and a prototype user interface was implemented as the precursor to a full scale decision support system. With technical research complete, the project focus now shifts to development of a commercial software product to provide users with actionable insight into water availability and the risk/resilience of critical systems at their locations of interest. Although DIVER-H was originally conceived as a tool for hydroelectric power applications, the same underlying technology can be readily applied to other water-consuming systems including coal, natural gas, oil, and nuclear power plants.

Chaudhary, Aashish [Kitware, Inc., Clifton Park, N

NUTRON NESHAPs Dashboard

My project aims to enhance the Nuclear Material Tracking Application (NUTRON) software by integrating a tool for the National Emission Standards for Hazardous Air Pollutants (NESHAP) emissions calculations and presenting this data on a dashboard. Inefficiencies in the current NESHAP calculation process were addressed, which will result in more timely regulatory compliance efforts. Key improvements include revising the transfer request system, incorporating effective dose calculations, and developing a data visualization dashboard into NUTRON. The project involved creating a wireframe, preparing an Engineering Calculations and Analysis Report (ECAR), stakeholder meetings, and providing supplemental documentation. Key findings indicate that the proposed modifications will streamline the NESHAP calculation process, reduce human error, and provide REC personnel with accurate and timely data for material use determinations and dose estimations. Future work focuses on completing the NUTRON modifications and fully integrating the new features, ensuring a more efficient and reliable system for tracking and reporting nuclear material transfers.

99 - GENERAL AND MISCELLANEOUS

Microgrid Hardening Design Toolkit User Guide: Software v0.29

Microgrid Hardening Design Toolkit helps microgrid stakeholders assess community-specific natural hazard risks to microgrid components and provides mitigation strategies to reduce those risks. Using census tract location inputs and the Federal Emergency Management Agency (FEMA) Risk Index dataset, the tool provides a ranked list of the highest risk hazards for a selected community and hazard-specific mitigation options for microgrid components. It also provides risk twin communities with similar hazard risk profiles and includes a radar-chart to visually compare risk profiles across communities. The toolkit is expected to help users quickly understand community-specific hazard risks and make decisions for microgrid hardening.

24 POWER TRANSMISSION AND DISTRIBUTION

Advancing \textit{otsdaq}: Enhancements for Usability, Accuracy, and Robustness

High-energy physics (HEP) experiments require data acquisition (DAQ) systems that can orchestrate complex detector operations, high data throughput, and responsive, real-time feedback to operators. Traditional DAQ stacks, which are often bespoke, command-line driven and highly specific, impose large learning curves on users. The Off-The-Shelf Data Acquisition (\textit{otsdaq}) framework was created to address these issues by offering a highly customizable and scalable browser-based ’desktop’ environment, in which experiment-specific control and monitoring applications can be easily deployed and integrated. Although the initial development of the \textit{otsdaq} software was aimed at the Fermilab Test Beam Facility, \textit{otsdaq} is now being leveraged for broader deployment, including the upcoming Mu2e experiment, where real-time monitoring of field-programmable gate array (FPGA)-based Data Transfer Controllers (DTCs), Clock and Fanout (CFO) boards, and several other subsystems are critical. We contribute a set of targeted improvements to \textit{otsdaq}: bitmap visualization functionality for configured data, improved and corrected delta-based DTC throughput metrics, version control (VC)-backed source navigation for console messages, custom navigation hooks to eliminate disruptive user interface glitches, and copy-to-clipboard support for macro execution history. These changes improve usability, reduce debugging time, and increase accuracy in performance data as Mu2e moves toward commissioning.

Mohammed, A. [Unlisted, US]

radkit base v1.6

The radkit (base) software suite (python) consists of three primary libraries: stark, trajan, and curie. The trajan library provides the tools to analyze and manipulate data from lidar and inertial measurement unit (IMU) devices, cameras, as well as trajectories from algorithms such as simultaneous localization and mapping (SLAM). These components allow reading and writing standard data formats, performing rigid affine transformations, discretizing three-dimensional space, and visualizing data products. The curie library comprises a standard set of object-oriented tools for radiation data and analysis in the following modules: (1) listmode and binmode data classes with methods for manipulation, plotting, slicing and file IO; (2) radiological/nuclear source detection/identification analysis results; (3) source encounters of correlated analyses and (4) energy-dependent angular detector response functions. The stark package provides low-level tools that are leveraged by both curie and trajan. The tools are flexible for offline analysis as well as performant for real-time integrations.

Salathe, Marco [Lawrence Berkeley National Laborat

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

HERO WEC V1.0 - WEC-Sim Model (July 2024)

**This submission supersedes submission MHKDR-483** This submission file contains the files that are needed to simulate NREL's HERO WEC (hydraulic and electric reverse osmosis wave energy converter). This requires the user to have already installed WEC-Sim. In addition to the standard toolboxes that are required to run WEC-Sim the user will also need the Simscape Fluids and Simscape Driveline packages. The zip file (HERO_V1_WECSim_2024.zip) contains the following: - HERO_HPTO_2024.slx: Simulink-based WEC Sim model of the first gen (V1.0) Hydraulic PTO (power take-off) that was designed for the HERO WEC. This model has been updated since submission #483 based on in-laboratory experimental results. - wecSimInputFile.m: Input file needed to run the model - userDefinedFunctionsMCR.m: MCR (multi condition run) script that is needed if a use wants to simulate multiple wave conditions. - geometry (folder): Includes the geometry file that is needed for visualization - hydroData (folder): Includes the required WAMIT data to run WEC-Sim -HydVisualization.mlx: Visualization script to plot simulation results (not needed to run)

16 TIDAL AND WAVE POWER

Advancing Building Energy Modeling with Large Language Models: Exploration and Case Studies

The rapid progression in artificial intelligence has facilitated the emergence of large language models like ChatGPT, offering potential applications extending into specialized engineering modeling, especially physics-based building energy modeling. This paper investigates the innovative integration of large language models with building energy modeling software, focusing specifically on the fusion of ChatGPT with EnergyPlus. A literature review is first conducted to reveal a growing trend of incorporating large language models in engineering modeling, albeit limited research on their application in building energy modeling. We underscore the potential of large language models in addressing building energy modeling challenges and outline potential applications including simulation input generation, simulation output analysis and visualization, conducting error analysis, co-simulation, simulation knowledge extraction and training, and simulation optimization. Three case studies reveal the transformative potential of large language models in automating and optimizing building energy modeling tasks, underscoring the pivotal role of artificial intelligence in advancing sustainable building practices and energy efficiency. The case studies demonstrate that selecting the right large language model techniques is essential to enhance performance and reduce engineering efforts. The findings advocate a multidisciplinary approach in future artificial intelligence research, with implications extending beyond building energy modeling to other specialized engineering modeling.

building energy modeling

The Analysis Description Language Ecosystem: Latest developments and physics applications

We present latest developments in Analysis Description Language (ADL), a declarative domain-specific language describing the physics algorithm of a HEP data analysis decoupled from software frameworks. Analyses written in ADL can be integrated into any framework for various tasks. ADL is a multipurpose construct with uses ranging from analysis design to preservation, reinterpretation, queries, visualisation, combination, etc. The most advanced infrastructure to execute ADL on events is the CutLang runtime interpreter. Recent technical developments include an automated interface with different data types, generation of the abstract syntax tree, a visualization tool that that auto-converts analysis flows to graphs, incorporation of trained machine learning models and a Jupyter-based plotting tool. We also report physics implications including a large scale LHC analysis implementation and validation effort for beyond the standard model reinterpretation purposes and studies with ATLAS and CMS open data.

Sekmen, Sezen [Kyungpook National Univ., Daegu (Ko

Effective Visualization of Radar Data for Users Impacted by Color Vision Deficiency

Color vision deficiency (CVD) is a decreased ability to discern between particular colors. Eight percent of genetic males and half a percent of genetic females have some form of CVD, with many in the radar community falling into this group. When presenting data on a two-dimensional plane, it is common to use colors to represent values via a colormap. Colormap choice in the radar community is influenced by the ability to highlight scientifically interesting features in data, institutional choices, and domain dominance of legacy colormaps. The problem with these current colormaps is that many do not project well for those with CVD (i.e., green next to red). In working with the CVD community to address this problem, multiple colormaps for moments such as equivalent reflectivity factor and Doppler velocity were created for users with forms of CVD such as deuteranomaly, protanomaly, protanopia, and deuteranopia using Python tools such as colorspacious and viscm. We show how these colormaps can improve interpretability for four cases: a mesoscale convective system, a pyrocumulonimbus storm, a wintertime midlatitude cyclone, and widespread storms with a large bird migration. These new radar equivalent reflectivity factor, Doppler velocity, and polarization colormaps are designed to highlight rain, frozen precipitation, nonmeteorological targets, and velocity-based items, are perceptually uniform, and are visually friendly for those with CVD.

54 ENVIRONMENTAL SCIENCES

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles

Electron Microscopy Studies of Soft Nanomaterials

This review highlights recent efforts on applying electron microscopy (EM) to soft (including biological) nanomaterials. We will show how developments of both the hardware and software of EM have enabled new insights into the formation, assembly, and functioning (e.g., energy conversion and storage, phonon/photon modulation) of these materials by providing shape, size, phase, structural, and chemical information at the nanometer or higher spatial resolution. Specifically, we first discuss standard real-space two-dimensional imaging and analytical techniques which are offered conveniently by microscopes without special holders or advanced beam technology. The discussion is then extended to recent advancements, including visualizing three-dimensional morphology of soft nanomaterials using electron tomography and its variations, identifying local structure and strain by electron diffraction, and recording motions and transformation by in situ EM. On these advancements, we cover state-of-the-art technologies designed for overcoming the technical barriers for EM to characterize soft materials as well as representative application examples. Here, the even more recent integration of machine learning and its impacts on EM are also discussed in detail. With our perspectives of future opportunities offered at the end, we expect this review to inspire and stimulate more efforts in developing and utilizing EM-based characterization methods for soft nanomaterials at the atomic to nanometer length scales in academic research and industrial applications.

Imaging

Large language model evaluation for high–performance computing software development

We apply AI-assisted large language model (LLM) capabilities of GPT-3 targeting high-performance computing (HPC) kernels for (i) code generation, and (ii) auto-parallelization of serial code in C ++, Fortran, Python and Julia. Our scope includes the following fundamental numerical kernels: AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG, and language/programming models: (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). Kernel implementations are generated using GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code given simple + + prompt variants. To quantify and compare the generated results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. For auto-parallelization, we use ChatGPT interactively giving simple prompts as in a dialogue with another human including simple “prompt engineering” follow ups. Results suggest that correct outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general-purpose Python can benefit from adding language keywords, while Julia prompts perform acceptably well for its Threads and CUDA.jl programming models. Finally, we expect to provide an initial quantifiable point of reference for code generation in each programming model using a state-of-the-art LLM. Overall, understanding the convergence of LLMs, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

97 MATHEMATICS AND COMPUTING

Diagnostic diagrams for ram pressure stripped candidates

ABSTRACT This paper presents a method for finding ram pressure stripped (RPS) galaxy candidates by performing a morphological analysis of galaxy images obtained from the Legacy survey. We consider a sample of about 600 galaxies located in different environments such as groups and clusters, tidally interacting pairs and the field. The sample includes 160 RPS previously classified in the literature into classes from J1 to J5, based on the increasing level of disturbances. Our morphological analysis was done using the astromorphlib software followed by the inspection of diagnostic diagrams involving combinations of different parameters like the asymmetry (A), concentration (C), Sérsic index (n), and bulge strength parameters $F(G,\, M_{20})$. We found that some of those diagrams display a distinct region in which galaxies classified as J3, J4, and J5 decouples from isolated galaxies. We call this region as the morphological transition zone and we also found that tidally interacting galaxies in pairs are predominant within this zone. Nevertheless, after visually inspecting the objects in the morphological transition zone to discard obvious contaminants, we ended up with 33 bona fide new RPS candidates in the studied nearby groups and clusters (Hydra, Fornax, and CLoGS sample), of which one-third show clear evidence of unwinding arms. Future works may potentially further increase significantly the samples of known RPS using such method.

Astronomy & Astrophysics

Digital Twin for Chemical Science (DTCS) v0.01

Directly visualizing the trajectories of chemistry can unravel novel insights into the behavior of catalysts, gas phase reactions, photo-induced dynamics, and building blocks for quantum information processing. The ability of explicitly identifying, tracking, and tagging the exchange of matter, hence the annihilation and creation of new chemical species, can be best realized through a close coupling of theory and experiment. While the synchrotron-based characterization facilities propelled rapidly in its hardware, providing higher brightness, better resolution, and more precision, the software infrastructure is lagging. We developed DTCS (Digital Twin for Chemical Science) v.01, a central platform that faithfully mimics advanced instrumentations in Scientific User Facilities, by solving a variety of technical challenges in data acquisition, analysis, and model-driven interpretation. Rooted in physics and accelerated by AI, we validated this concept by direct comparison with precise experimental X-ray Photoelectron Spectroscopy (XPS) observations using a ubiquitous metal-water interfacial scenario, i.e., Ag/H2O as our main narrative. The DTCS v.01 input mirrors how the bench chemists work, with the output directly linked to the end station computer, thereby providing a user-friendly, knowledge-driven, and accessible user experience with mechanistic insights standardized in a way that are ready to be published, versioned, and transferred flexibly.

Qian, Jin

Data & Code from Phoenix CPPP Phase 2 Analysis

This data and code package supports the analysis presented in “Beyond Surface Cooling: Comprehensive Field Assessment of Reflective Pavement Thermal Performance in Phoenix, Arizona” and provides fully reproducible workflows for evaluating the thermal performance of cool pavement treatments in a hot urban environment. The dataset integrates multi-modal field measurements collected across residential and nonresidential settings, including mobile air temperature traverses, stationary air temperature monitoring, residential mean radiant temperature (MRT) measurements, subsurface temperature profiles, and controlled testbed observations. The data package contains raw and processed datasets in comma-separated value (CSV) format, accompanying metadata files describing site characteristics and measurement protocols, and R scripts (.R files) used for data cleaning, time synchronization, spatial and temporal matching, quality control filtering, statistical comparison, and figure generation. All analyses were conducted using R (version ≥ 4.2.0) with commonly available packages (e.g., tidyverse, lubridate, data.table, ggplot2). No proprietary software is required to reproduce results. Field campaigns were designed to quantify the effects of high-reflectance pavement coatings on surface temperature, near-surface air temperature, subsurface heat propagation, and radiative heat exposure. Temporal alignment procedures include standardized timestamp conversion and nearest-neighbor matching of high-frequency sensor measurements to stop-based metadata within defined tolerance windows to ensure comparability across instruments. The workflows generate summary statistics, treatment–control contrasts, depth-dependent thermal gradients, and time-series visualizations used in the associated publication. By integrating mobile, stationary, radiative, and subsurface measurements within a unified and transparent processing framework, this package enables comprehensive evaluation of cool pavement performance across multiple thermal exposure pathways and supports reuse in future urban heat mitigation and climate resilience studies.

AIR TEMPERATURE

ACTIVE

The Automated Control Testbed for Integration, Verification, and Emulation (ACTIVE) framework is a software platform designed to support the optimized operation and management of a wide range of building types. It enables the development, testing, and validation of diverse control strategies, including AI-based, rule-based, and model-based approaches. The platform facilitates a seamless transition from simulation-based evaluation of control strategies to real-world field validation and deployment. ACTIVE supports the full building management lifecycle, encompassing data acquisition and management, system monitoring, optimized control, adaptive learning services, device dispatch and coordination, as well as advanced analytics and visualization. Together, these capabilities provide an integrated environment for improving building performance, operational efficiency, reducing energy cost, and reliability.

Smith, Robert [Oak Ridge National Laboratory (ORNL