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At least 631 records · Page 35

Datum: A Scientific Metadata Catalog

The data catalog market is currently flooded with a myriad of different products, but none serve the scientific community well. There are cloud-native tools like Databricks, Snowflake,to on-premise solutions like Collibra and Datahub. The common failing of all these tools however, is their inability to serve the scientific data community directly. Most catalogs are targeted towards financial, health, or user data - not sensor or scientific domain data. They also prioritize integrations that often don’t exist or are just starting to be used in the scientific realm - all while ignoring common scientific tools and file types. Datum is a catalog which targets the scientific data directly, including the tools and networks in which those tools are used. We work with the producers and consumers of the data where they are, targeting cloud and on-premise with a focus on classified networks. Datum is an Erlang/Elixir application. Technical Features Note: The features listed below are still under development and may change, slightly, upon final delivery of the product. File Formats - Datum has the ability to read additional metadata and provides processing pipelines for the following file formats: Plain Text, PDF, LaTeX, HTML, Open Document Format (.odt), XML, CSV/TSV (and other standard delimiters), OpenDocument Database and Spreadsheets, Geo-Referenced TIFF, Common Data Format, HDF/HDF5, LabView TDMS, Excel, DeltaTables, Parquet, Apache Iceberg, Apache Hudi and many others. Metadata Collection - Scanners for the local and networked file systems and cloud storage providers. Network integration with common databases such as MSSQL and MySQL. User Plugin System - Users are able to provide either file processing, metadata extraction, or sampling plugins in the programming language of their choice. Authentication/Authorization -: OIDC integration, SCIM provisioning and EntraID integration out of the box. Full user and group management system with a “least privilege” operating mode. Governance - Customizable data governance platform; dictate and enforce required metadata, enforce data embargos, and enforce user agreements and NDAs before data access. Ability to create health checks on data, rejecting abandoned or poorly curated data and automatically removing it from the search index. Ability for users to submit corrections. Search - Semantic search is a first class citizen. No licenses to expensive, external software required. Integrated use of vectors and vector-based search allows for AI agent integration at all levels of operation. Metadata Model - Display and control data’s lineage and connections to other data and data directories. Data is modeled after a filesystem - an organization instantly recognizable and navigable by most any user. CLI and SDK - Ships with a Command Line Interface (CLI) tool and with a fully-featured Python SDK. This allows for rapid and programmatic use of Datum by every level of user. Minimal Infrastructure - Datum ships as a single executable file and can be run on any operating system and most CPU architectures. Datum has no reliance on external databases, search indexing tools, or other outside services - and it runs equally well on edge computing devices, cloud services, or in a clustered HPC environment.

darrington, john↗

Big-data Efficient and Automated Science Transfer (BEAST): An Open-Source Software Architecture for Arc Jet Data Management, Modeling, and Automation

Big-data Efficient and Automated Science Transfer (BEAST) is a facility data management application developed for the NASA Ames arc jet facilities. The current decentralized data management practices limit statistical tracking, synchronization between video/time series, search capability, data throughput, and data processing speed/efficiency. Consequently, BEAST was developed to provide a new data infrastructure with streamlined data collection, processing, transfer, and analysis. This new framework also seeks to implement the FAIR principles of data stewardship: Findable, Accessible, Interoperable, and Reusable. The BEAST framework is based on a combination of the Python Django web framework and the Python data stack to provide a monolithic, open-source platform for data management, automation, and machine learning. This architecture was chosen for maintainability and scalability for a small, in-house development team. This paper will describe the application framework, deployment, and discuss the benefits and future plans for the system.

Data management↗

Developing and testing capabilities for simulating cases with heterogeneous land/water surfaces in a novel atmospheric large eddy simulation code

Large eddy simulations (LES) are the primary computational tool used to simulate high Reynolds number three-dimensional turbulent flows. In the context of earth system sciences, particularly atmospheric science, LES are uniquely able to resolve the scales of atmospheric motion that are key for building process-level understanding of boundary layer turbulence, atmosphere-surface interaction, clouds, and cloud-aerosol-chemistry interaction, and are a core limited-area modeling capability. Increasing demands are being placed on LES code bases as growing high performance computing resources allow LES to address a wider range of scientific problems. In addition, LES are emerging as a source of high-quality machine learning training data. These demands necessitate an agile and extensible code base that allows the model to quickly adapt to emergent needs. However, LES have largely relied on legacy Fortran code bases that lack flexibility. A new, Python-based LES capability called Predicting INteractions of Aerosol and Clouds in Large Eddy Simulation (PINACLES) has been developed as part of the Department of Energy’s Earth System Model Development (ESMD) program area’s Enabling Aerosol-cloud interactions at Global convection-permitting scalES (EAGLES) project. PINACLES was developed from the ground up with a philosophy of maximizing scientific throughput, by attempting to optimize for both model throughput and software extensibility. The initial development of PINACLES delivered a state-of-the-art idealized LES capability solving the non-hydrostatic anelastic equations of motion with doubly periodic boundary conditions and idealized homogenous surface boundary conditions. Here we provide a final report on the outcomes of a fiscal year 2021 Seed Laboratory Directed Research Project that extended PINACLES in two key ways. First, PINACLES was coupled to a state-of-the-art land surface model enabling it to simulate spatially inhomogeneous land-atmosphere interactions that are known to control key atmospheric processes. Second, the dynamical core of PINACLES was modified to permit non-periodic boundary conditions. This model enhancement enables simulation of realistic cases with boundary conditions prescribed from atmospheric reanalysis and enables nested simulations conducted on a hierarchy of computational domains with increasing resolution. Together, these extensions to PINACLES make it a formidable modeling capability and expand its potential application to diverse components of DOE’s atmospheric science portfolio.

42 ENGINEERING↗

AIMSim : An accessible cheminformatics platform for similarity operations on chemicals datasets

The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Further, most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

braggedgemodeling

braggedgemodeling (bem) is an open-source Python package for modeling neutron Bragg-edge imaging. It computes the wavelength-dependent total neutron cross-section of a material (coherent and incoherent elastic, coherent and incoherent inelastic scattering, and absorption) from its crystal structure, and implements the March-Dollase texture model and the Jorgensen peak profile, supporting quantitative analysis of energy-resolved neutron imaging data (phase, stress/strain, and texture). Published in the Journal of Open Source Software (2018).

Lin, Jiao [Oak Ridge National Laboratory (ORNL), O↗

Europa Clipper Payload Verification and Validation: Avionics-Instrument Interface Test Campaign

NASA's Europa Clipper mission will investigate Jupiter's icy moon Europa using a payload suite consisting of nine instruments to address a range of scientific objectives concerning Europa's habitability. As the project proceeds past its Critical Design Review, confidence is being built in the system's ability to achieve mission objectives through the implementation of a rigorous payload verification and validation (V&V) program. As part of this payload V&V program, instrument box-level testing was performed by the payload team to verify select instrument-avionics interface requirements. This testing was performed at JPL using the avionics testbed's Bulk Data Storage Emulator (BDSEM) with visiting instrument Test Models. This paper summarizes the Data Link test campaign involving roughly four days of functional testing per instrument, including planning, testing methods, types of issues found, and the requirement closure process. Detail is also provided on the development, deployment, and validation of a standardized analysis tool used in data reviews. This testing verified requirements related to commanding rates, loss of link, packet format, clock counters, loopback test capability, and SpaceWire jitter and skew margins. Additional risk reduction testing of basic commanding, counter behavior, science data collection and transfer, and interface swapping was also performed. Because the BDSEM venue was not originally designed to be a run for record venue, the process of characterizing venue fidelity and establishing suitability for requirement closure using data collected in this venue will also be addressed.In order to close requirements, an extensible tool was developed to post-process instrument command and telemetry data from their original binary to a human-readable format and give visibility to errors detected within the data, such as packets with Cyclic Redundancy Check errors. This tool, called payload-packet-parser, is a Python 3.9 command line tool built using a variety of open-source Python libraries. Payload-packet-parser was designed to support parsing command and telemetry packets for all Europa Clipper instruments and additional analysis tools were developed for verification of specific information interface requirements. This test campaign, including post-processing using a single parsing and verification toolset, allowed for early interface testing, alleviating testing burdens on instrument teams and buying down risk on the instrument-avionics interface by finding hardware and software issues and idiosyncrasies prior to integration with system test venues. Over twenty issues were discovered across the payload, resulting in software updates and instrument rework well in advance of any system impacts. This paper concludes with an assessment of benefits and costs of this type of testing and lessons learned.

Montanez, Leticia↗

An end-to-end workflow for executing a classically bootstrapped variational quantum algorithm on an academic quantum computer

Academic quantum computing platforms often face unique challenges in executing quantum workloads due to fragmented software environments and limited engineering support. Unlike commercial ecosystems, academic devices typically evolve without full-stack integration in mind, making it difficult to run complex applications—such as variational quantum algorithms (VQA)—reliably and efficiently. Issues such as incompatible software layers and lack of automated job management significantly increase the overhead of theory-experiment collaboration. To address these challenges, we develop a modular, end-to-end workflow that decouples application-layer code from low-level hardware control, automates circuit submission and result collection, and supports fine-grained circuit-level job scheduling and recovery. The architecture employs a dual-end application programming interface (API) design, enabling robust operation across unstable or resource-constrained hardware backends. For practical use, the framework is lightweight and user-friendly, allowing rapid prototyping of full-stack workflows using basic Python tools. We validate this workflow on a high-fidelity trapped-ion quantum computer by demonstrating a variational quantum eigensolver (VQE) experiment with a classically bootstrapped ansatz initialization technique. The system successfully executed over 60,000 circuits across multiple molecular test cases with minimal human intervention, highlighting the framework’s effectiveness in enabling reproducible, resilient quantum experimentation in academic settings.

Clifford↗

TEAMER: Crossflow Turbine Fairing Geometry Optimization - Report and CFD Modeling Files

The dataset includes computational fluid dynamics (CFD) models and simulation files for crossflow turbines as well as a detailed project report. The report documents the project undertaken by the Ocean Renewable Power Company (ORPC) to design and optimize a modular fairing for the Modular RivGen Marine Hydrokinetic (MHK) turbine, which enhances the efficient deployment and operation of turbine arrays. The project focused on optimizing the hydrodynamic performance of the fairing using CFD, with an emphasis on two key geometric parameters: the fairing's cross-sectional shape and the spacing between the rotor and the fairing. The analysis aimed to maximize net power output while also assessing discretized loading to evaluate ultimate and fatigue loads on the turbine components. The numerical modeling was conducted using both the commercial CFD software Star-CCM+ and the open-source code openFOAM, with the latter utilizing the actuator line library, turbinesFOAM. This dual-code approach was intended to increase confidence in the results and demonstrate the viability of using open-source tools for high-fidelity marine energy modeling. This dataset includes all necessary files for actuator line simulations in openFOAM, as well as 2D blade-resolved CFD results, along with Python and Java scripts for setting up and post-processing simulations.

16 TIDAL AND WAVE POWER↗

Catalyst Design in Nitrate Removal

Based on the volcano plot developed by Dr. Goldsmith group (Report linked in submission), we utilized DFT (density functional theory) calculations to search for bimetallic materials in the application of catalysts in aqueous nitrate removal. The calculations are conducted via the high-throughput automated workflow package developed by our group (Github linked in submission) using VASP commercial first-principles calculation software.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

An automated fast neutron computed tomography instrument with on-line focusing for non-destructive evaluation

A fast neutron tomography imaging instrument has been designed, built, and tested at The Ohio State University 500 kW Research Reactor on a fast neutron beamline with a peak neutron flux ≈5.4 × 107 n·cm−2·s−1 at 1.6 MeV median neutron energy. The instrument and beamline are also configurable for thermal neutron imaging. The imaging apparatus is composed of a lens coupled, water-cooled Electron Multiplying Charge Coupled Device camera, a front-surface mirror, and a high light yield plastic Polyvinyl toluene scintillator. The instrument sits on a mobile cart. A total of 5 motion-control stages are built into the system for XYZ and rotational degrees of freedom for sample positioning; the fifth stage fine tunes the focal distance between the camera and the scintillator to achieve on-line focusing. A Python code with a user-friendly graphical user interface controls the fully automated image acquisition, not requiring user interaction, yet facilitating tracking of the image acquisition. A complete fast neutron computed tomography dataset with 360 projections requires less than 3 h, with 30 s per projection. On-line focusing is accomplished with a commercial, off-the-shelf, dielectrically actuated liquid lens. Finally, tomographic reconstructions are visualized using the Livermore Tomography Tools software package. The effective pixel size (width and height) is ≈0.1058 mm, yielding a minimum voxel size of 0.1058 × 0.1058 × 0.1058 mm3, and produces a spatial resolution of 231 μm when calculated from knife-edge measurements.

Bisbee, M. G. (ORCID:0000000313466697)↗

Python Based Plume Dynamics Estimation Tool (PyPDET) Rapid Plume Strike Analysis for RPOD Maneuvers in Deep Space Operations

I worked as a NASA Intern during the Summer 2023 term in the DS-00 division under the supervision of my mentor, Dr. Jonathan Pitt. Our goal was to build on our previous work from 2022 to develop a plume strike estimation tool using a prescribed physics methodology and model plume impingement effects while considering the dynamics of a rendezvous, operations, proximity, and docking (RPOD) maneuver. This tool supports previously configured CFD-DSMC calculations by allowing for rapid analysis of initial designs using a low-fidelity source flow model. Engineers can then use the high-fidelity CFD-DSMC tool to consolidate results as they work towards finalizing a design. This year’s project was focused on developing a software application that other engineers would be using in their analysis. Thus, the user’s experience was considered in the development of this application. Proper documentation, testability, and modularity of the codebase was our priority. For example, the project included auto documentation procedures to start building towards a User Manual, while also including dedicated demonstration cases for more explicit communication of functionality. Also, this project included a framework for testing the source code for future developments. Additionally, care was taken to develop the code using an Object-Oriented Programming approach. Thus, allowing for a modular extensibility of functionality in anticipation of future developments. The core work of this project was developing an algorithm that would transform the visiting vehicle and associated thruster data according to the kinematics described in the jet firing history. It would then calculate the estimated plume strikes on two of the target vehicles and write data accordingly into a VTK file. Summer work is to conclude by developing and presenting a PowerPoint slide deck at the intern exit briefing on August 11 th , 2023. Once the model for simple plume strike calculations is developed and tested there are several avenues to explore to continue development of this tool. These are also discussed in this report.

Plume Impingement↗

Preferred Practices Through a Project Template

In the realm of scientific software development, adherence to best practices is often advocated. However, implementing these can be challenging due to differing opinions. Certain aspects, such as software licenses and naming conventions, are typically left to the discretion of the development team. Our team has established a set of preferred practices, informed by, but not limited to, widely accepted best practices. These preferred practices are derived from our understanding of the specific contexts and user needs we cater to. To facilitate the dissemination of these practices among our team and foster standardization with collaborating domain scientists, we have created a project template for Python projects. This template serves as a platform for discussing the implementation of various decisions. This paper will succinctly delineate the components that constitute an effective project template and elucidate the advantages of consolidating preferred practices in such a manner.

Zhang, Chen↗

Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

QForte: An Efficient State-Vector Emulator and Quantum Algorithms Library for Molecular Electronic Structure

Here, we introduce a novel open-source software package QForte, a comprehensive development tool for new quantum simulation algorithms. QForte incorporates functionality for handling molecular Hamiltonians, fermionic encoding, ansatz construction, time evolution, and state-vector emulation, requiring only a classical electronic structure package as a dependency. QForte also contains black-box implementations of a wide variety of quantum algorithms, including variational and projective quantum eigensolvers, adaptive eigensolvers, quantum imaginary time evolution, and quantum Krylov methods. We highlight two features of QForte: (i) how the Python class structure of QForte enables the facile implementation of new algorithms, and (ii) how existing algorithms can be executed in just a few lines of code.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DeepDiagnostics: A Software Package for Streamlined Posterior Evaluation

Automated prediction techniques like simulation-based inference (SBI) are important tasks for science experiments that produce large amounts of complex, raw data. However, their development remains in its early stages because the uncertainties of these techniques lack sufficient trustworthiness and interpretability. Packages for SBI provide a growing set of diagnostics; however, the software requirements are substantial, as they are tied to the inference technology itself, and the APIs lack adaptability. We introduce the DeepDiagnostics package for diagnosing posteriors from analytic likelihood-based methods and SBI methods, such as neural posterior estimation. DeepDiagnostics produces a comprehensive set of high-quality visualizations and metrics in a highly accessible, easy-to-use, and flexible package. We address all of these goals by providing a command-line inference tool and a Python API that is controlled through a configuration file. The package includes common diagnostics, such as parity plots, corner (covariance) plots, simulation-based calibration (SBC) diagnostics (including posterior coverage and rank histograms), Lemos et al. s PQMass and TARP, Masserano et al. s WALDO, Linhart et al. s LC2ST, as well as credible region diagnostics developed by our group.

Voetberg, Maggie [Fermilab]↗

Truchas Overview

Truchas and Truchas-PBF are two sister codes for part-scale multi-physics modeling of manufacturing processes. Both programs are open source and made publicly available. They’re designed for efficient use of HPC resources and can be programmatically driven from Python packages. This enables automatic execution and analysis of ensembles of simulations, in some cases allowing 1000s of simulations to be evaluated in a day on HPC. Beyond just giving engineers a window into the concealed internal state of a system, the goal of Truchas is to provide a framework for developing novel manufacturing processes by understanding how the entire space of engineering inputs affects thermal state. It often is used to explore combinations of capabilities uncommon in commercial software, or to scale up analyses beyond the capabilities of commercial software.

97 MATHEMATICS AND COMPUTING↗

A Python Library for Radiance Matrix-based Simulation Control and EnergyPlus Integration

Radiance matrix-based methods enable efficient parametric simulations, allowing users to vary sky conditions, fenestration systems, and other model parameters at a minimal cost to computation. However, the steep learning curve and complex workflow hinder the widespread adoption of matrix-based methods. The frads Python library with a series of command-line tools was developed to automate the entire matrix-based simulation process, lowering entry barriers and reducing human error. Co-simulation between EnergyPlus and Radiance was also enabled using the Python library from EnergyPlus. Key Innovations • Command-line based automation of Radiance matrix-based simulation methods • Python library facilitates broader adoption of Radiance matrix-based simulation methods • Radiance EnergyPlus run-time integration enabling the modeling of advanced control systems Practical Implications The frads library, with associated command-line tools, provides practitioners with the capability to easily adopt and use Radiance matrix-based simulation methods for various daylighting, solar control, and energy-related evaluations. Frads' current form is designed for 1) users familiar with a command-line interface and 2) software developers to integrate the matrix-based methods into existing software packages.

Wang, Taoning↗

A Tool for Defining Tow-Steered Laminates for Finite Element Grids

Tailoring of composite laminates is traditionally performed by changing the orientation of straight fibers in one or more plies. Modern automated fiber placement machines facilitate placement of bundles of curved fibers (tows) in a process called tow-steering, but additional variables must be used to define the shapes of tow-steered fiber paths. In this paper, a Python-based tool, called Automated Tool for Steered COmposite Optimizable Laminates (ATSCOOL), is presented for modeling steered tows as chains of circular arcs. The geometry for defining tow path shapes using four input variables is described. The formulae for determining gaps and overlaps between clusters of consecutive tows, called courses, and for determining the number of steered courses needed to cover a rectangular panel are presented. Graphical representation of courses and thickness distribution in an example panel using the ATSCOOL software are presented. Finally, an example of a finite element analysis performed using the property information output from ATSCOOL is shown.

finite element analysis↗