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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

SU-G-TeP4-06: An Integrated Application for Radiation Therapy Treatment Plan Directives, Management, and Reporting

Purpose: With electronic medical records, patient information for the treatment planning process has become disseminated across multiple applications with limited quality control and many associated failure modes. We present the development of a single application with a centralized database to manage the planning process. Methods: The system was designed to replace current functionalities of (i) static directives representing the physician intent for the prescription and planning goals, localization information for delivery, and other information, (ii) planning objective reports, (iii) localization and image guidance documents and (iv) the official radiation therapy prescription in the medical record. Using the Eclipse Scripting Application Programming Interface, a plug-in script with an associated domain-specific SQL Server database was created to manage the information in (i)–(iv). The system’s user interface and database were designed by a team of physicians, clinical physicists, database experts, and software engineers to ensure usability and robustness for clinical use. Results: The resulting system has been fully integrated within the TPS via a custom script and database. Planning scenario templates, version control, approvals, and logic-based quality control allow this system to fully track and document the planning process as well as physician approval of tradeoffs while improving the consistency of the data. Multiple plans and prescriptions are supported along with non-traditional dose objectives and evaluation such as biologically corrected models, composite dose limits, and management of localization goals. User-specific custom views were developed for the attending physician review, physicist plan checks, treating therapists, and peer review in chart rounds. Conclusion: A method was developed to maintain cohesive information throughout the planning process within one integrated system by using a custom treatment planning management application that interfaces directly with the TPS. Future work includes quantifying the improvements in quality, safety and efficiency that are possible with the routine clinical use of this system. Supported in part by NIH-P01-CA-059827.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Reproducible, Component-based Modeling with TopoFlow, A Spatial Hydrologic Modeling Toolkit

Modern geoscientists have online access to an abundance of different data sets and models, but these resources differ from each other in myriad ways and this heterogeneity works against interoperability as well as reproducibility. The purpose of this paper is to illustrate the main issues and some best practices for addressing the challenge of reproducible science in the context of a relatively simple hydrologic modeling study for a small Arctic watershed near Fairbanks, Alaska. This study requires several different types of input data in addition to several, coupled model components. All data sets, model components and processing scripts (e.g. for preparation of data and figures, and for analysis of model output) are fully documented and made available online at persistent URLs. Similarly, all source code for the models and scripts is open-source, version controlled and made available online via GitHub. Each model component has a Basic Model Interface (BMI) to simplify coupling and its own HTML help page that includes a list of all equations and variables used. The set of all model components (TopoFlow) has also been made available as a Python package for easy installation. Three different graphical user interfaces for setting up TopoFlow runs are described, including one that allows model components to run and be coupled as web services.

58 GEOSCIENCES↗
DOE OSTI2017

Simulation of Precipitation Extremes Using a Stochastic Convective Parameterization in the NCAR CAM5 Under Different Resolutions

With the incorporation of the Plant-Craig stochastic deep convection scheme into the Zhang-McFarlane deterministic parameterization in the Community Atmospheric Model version 5 (CAM5), its impact on extreme precipitation at different resolutions (2°, 1°, and 0.5°) is investigated. CAM5 with the stochastic deep convection scheme (experiment (EXP)) simulates the precipitation extreme indices better than the standard version (control). At 2° and 1° resolutions, EXP increases high percentile (>99th) daily precipitation over the United States, Europe, and China, resulting in a better agreement with observations. However, at 0.5° resolution, due to enhanced grid-scale precipitation with increasing resolution, EXP overestimates extreme precipitation over southeastern U.S. and eastern Europe. The reduced biases in EXP at each resolution benefit from a broader probability distribution function of convective precipitation intensity simulated. Among EXP simulations at different resolutions, if the spatial averaging area over which input quantities used in convective closure are spatially averaged in the stochastic convection scheme is comparable, the modeled convective precipitation intensity decreases with increasing resolution, when gridded to the same resolution, while the total precipitation is not sensitive to model resolution, exhibiting some degree of scale-awareness. Sensitivity tests show that for the same resolution, increasing the size of spatial averaging area decreases convective precipitation but increases the grid-scale precipitation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

The structure of quantum singularities on a Cauchy horizon

Spacetime singularities pose a long-standing puzzle in quantum gravity. Unlike Schwarzschild, a generic family of black holes gives rise to a Cauchy horizon on which, even in the Hartle-Hawking state, quantum observables such as ⟨T μν ⟩ — the expectation value of the stress-energy tensor — can diverge, causing a breakdown of semiclassical gravity. Because they are diagnosed within quantum field theory (QFT) on a smooth background, these singularities may provide a better-controlled version of the spacetime singularity problem, and merit further study. Here, I highlight a mildness puzzle of Cauchy horizon singularities: the ⟨T μν ⟩ singularity is significantly milder than expected from symmetry and dimensional analysis. I address the puzzle in a simple spacetime ${\mathcal{W}}_P$, which arises universally near all black hole Cauchy horizons: the past of a codimension-two spacelike plane in flat spacetime. Specifically, I propose an extremely broad QFT construction in which, roughly speaking, Cauchy horizon singularities originate from operator insertions in the causal complement of the spacetime. The construction reproduces well-known outer horizon singularities (e.g., in the Boulware state), and remarkably, when applied to ${\mathcal{W}}_P$, gives rise to a universal mild singularity structure for robust singularities, ones whose leading singular behavior is state-independent. I make non-trivial predictions for all black hole Cauchy horizon singularities using this, and discuss extending the results beyond robust singularities and the strict near Cauchy horizon limit.

black holes↗
DOE OSTI2019

DCA++: A software framework to solve correlated electron problems with modern quantum cluster methods

We present the first open release of the DCA++ project, a high-performance research software framework to solve quantum many-body problems with cutting edge quantum cluster algorithms. DCA++ implements the dynamical cluster approximation (DCA) and its DCA extension with a continuous self-energy. The algorithms capture nonlocal correlations in strongly correlated electron systems, thereby giving insight into high-$T_c$ superconductivity. The code’s scalability allows efficient usage of systems at all scales, from workstations to leadership computers. With regard to the increasing heterogeneity of modern computing machines, DCA++ provides portable performance on conventional and emerging new architectures, such as hybrid CPU–GPU, sustaining multiple petaflops on ORNL’s Titan and CSCS’ Piz Daint supercomputers. Moreover, we show how sustainable and scalable development of the code base has been achieved by adopting standard techniques of the software industry. These include employing a distributed version control system, applying test-driven development and following continuous integration.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Multi-variable mathematical models for the air-cathode microbial fuel cell system

This research adopted the version control system into the model construction for the single chamber air-cathode microbial fuel cell (MFC) system, to understand the interrelation of biological, chemical, and electrochemical reactions. The anodic steady state model was used to consider the chemical species diffusion and electric migration influence to the MFC performance. In the cathodic steady state model, the mass transport and reactions in a multi-layer, abiotic cathode and multi-bacteria cathode biofilm were simulated. Transport of hydroxide was assumed for cathodic pH change. This assumption is an alternative to the typical notion of proton consumption during oxygen reduction to explain elevated cathode pH. The cathodic steady state model provided the power density and polarization curve performance results that can be compared to an experimental MFC system. Another aspect we considered was the relative contributions of platinum catalyst and microbes on the cathode to the oxygen reduction reaction (ORR). We found simulation results showed that the biocatalyst in a cathode that includes a Pt/C catalyst likely plays a minor role in ORR, contributing up to 8% of the total power calculated by the models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Continuous Integration Service at Fermilab

This paper describes the current architecture of Continuous Integration (CI) service developed at Fermilab, encountered successes and difficulties, as well as future development plans. The current experiment code has hundreds of contributors that provide new features, bug fixes, and other improvements. Version control systems help developers to collaborate in contributing software for their experiments, while the CI system helps developers keep their code healthy. The Fermilab CI service allows experiments and projects to test and validate their offline production and analysis code on the supported platforms. It is built on top of Jenkins, designed to be set up from a configuration file that provides implementation for each phase of the CI workflow, and able to validate experiment code through grid jobs. This CI service provides a dashboard for easy access to logs and statistical graphs. Since the CI service has been adopted by Fermilab experiments/projects, it proved to be very useful to intercept issues in their code early on and get them fixed before running it in production. Currently the CI service is in use by the ArgoNeuT, DUNE, g-2, LArIAT, MINERvA, mu2e, NOvA, SBND and uBooNE experiments and by the following projects: ART and LArSoft software suites, GENIE, and Glidein-WMS. The CI service is under active development and planning to support code profiling.

Di benedetto, Vito↗
DOE OSTI2015

Software management for the NO ν A Experiment

The NO$\nu$A software (NO$\nu$ASoft) is written in C++, and built on the Fermilab Computing Division's art framework that uses ROOT analysis software. NO$\nu$ASoft makes use of more than 50 external software packages, is developed by more than 50 developers and is used by more than 100 physicists from over 30 universities and laboratories in 3 continents. The software builds are handled by Fermilab's custom version of Software Release Tools (SRT), a UNIX based software management system for large, collaborative projects that is used by several experiments at Fermilab. The system provides software version control with SVN configured in a client-server mode and is based on the code originally developed by the BaBar collaboration. In this paper, we present efforts towards distributing the NO$\nu$A software via the CernVM File System distributed file system. Here, we will also describe our recent work to use a CMake build system and Jenkins, the open source continuous integration system, for NOASoft.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

MAUS: the MICE analysis user software

The Muon Ionization Cooling Experiment (MICE) collaboration has developed the MICE Analysis User Software (MAUS) to simulate and analyze experimental data. It serves as the primary codebase for the experiment, providing for offline batch simulation and reconstruction as well as online data quality checks. The software provides both traditional particle-physics functionalities such as track reconstruction and particle identification, and accelerator physics functions, such as calculating transfer matrices and emittances. The code design is object orientated, but has a top-level structure based on the Map-Reduce model. This allows for parallelization to support live data reconstruction during data-taking operations. MAUS allows users to develop in either Python or C++ and provides APIs for both. Various software engineering practices from industry are also used to ensure correct and maintainable code, including style, unit and integration tests, continuous integration and load testing, code reviews, and distributed version control. The software framework and the simulation and reconstruction capabilities are described.

47 OTHER INSTRUMENTATION↗
DOE OSTI2016

Running an open experiment: transparency and reproducibility in soil and ecosystem science

Researchers in soil and ecosystem science, and almost every other field, are being pushed--by funders, journals, governments, and their peers--to increase transparency and reproducibility of their work. A key part of this effort is a move towards open data as a way to fight post-publication data loss, improve data and code quality, enable powerful meta- and cross-disciplinary analyses, and increase trust in, and the efficiency of, publicly-funded research. Many scientists however lack experience in, and may be unsure of the benefits of, making their data and fully-reproducible analyses publicly available. Here we describe a recent "open experiment", in which we documented every aspect of a soil incubation online, making all raw data, scripts, diagnostics, final analyses, and manuscripts available in real time. We found that using tools such as version control, issue tracking, and open-source statistical software improved data integrity, accelerated our team's communication and productivity, and ensured transparency. There are many avenues to improve scientific reproducibility and data availability, of which is this only one example, and it is not an approach suited for every experiment or situation. Nonetheless, we encourage the communities in our respective fields to consider its advantages, and to lead rather than follow with respect to scientific reproducibility, transparency, and data availability.

global change↗
DOE OSTI2024

SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network

ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

Microbiology↗
DOE OSTI2014

Git Replacement for the

GRAPE is a tool for managing software project workflows for the Git version control system. It provides a suite of tools to simplify and configure branch based development, integration with a project's testing suite, and integration with the Atlassian Stash repository hosting tool.

Robinson, P.↗
DOE OSTI2018

ALS/Milo: BL402 RSXD data analysis

Suite of tools designed to simply data collection, extraction, reduction, and plotting for resonant soft x-ray scattering experiments performed at ALS beamline 4.0.2; speeds up the process of converting data into meaningful information for users to publish experimental results. * Python software routines for processing CCD images, including reciprocal space maps, diffraction peak alignment, resonant spectral profiles, line-cut comparisons, coordinate transforms, etc. * Scan file generator, optimized for typical uses cases, reduces burden on users by handling complex operations behind the scenes of a simplified user interface * Deployed at beamline endstation computers; packaged and deployable as standardized PyPI package * Under version control (git) and hosted on LBL-sponsored repository (bitbucket)

Shafer, Padraic↗
DOE OSTI2022

High Performance Computing Innovation Center Open Source Developer Tools

The High Performance Computing Innovation Center (HPCIC) aims to ease the transition for developers to use open source software provided by the lab. HPCIC Developer Tools is a collection of software, containers, cloud configurations, and associated documentation that make it easy to deploy tutorials or small apps to demonstrate lab-developed software. For example, building a tutorial container that includes lab software and interactive interfaces; a command line or web-based tool that accepts user preferences for the tutorial; supporting tools and software development kits (SDKs) for developer interactions or productivity in different languages embraced by the larger developer community such as Go, Rust, and Python; and automation in version control to support continued update of software and associated resources. These tools are best developed in an open source environment such as GitHub, not only to champion the lab's open source software, but for purposes of branding and demonstrating the lab's leadership in open source. Such an effort that brings in more developers to use and contribute to lab software can further improve the quality of the software, and developer experience at the lab.

Beckingsale, DavidA↗
DOE OSTI2023

Reposcanner

SAND2023-05455O Reposcanner provides a highly modular, extensible framework for defining routines for mining data from software repositories and performing analyses on that data to yield valuable insights on team behaviors. Reposcanner features seamless support for different version control platforms like GitHub, Gitlab, and Bitbucket; smart parsing of URLs; intelligent credential management capabilities; and a comprehensive test suite. Reposcanner is connected to the Exascale Computing Project and is intended for research purposes.

Mundt, Miranda↗
DOE OSTI2020

ames-market/psst

Python version of the AMES Wholesale Power Market Test Bed; no GUI. Previously hosted by Iowa State University; PNNL has assumed hosting. AMES existed in a non-version controlled and inconsistent form. PNNL added price-sensitive loads for transactive systems, with various other bug fixes and features.

McDermott, Tom↗
DOE OSTI2022

Repometer v.1.0

SAND2022-4256 O Online version control platforms offer insight into traffic and engagement with source code repositories, but only in limited ways and over short windows of time. Scientific software teams at Sandia National Laboratories and elsewhere want to collect and store engagement data to help tell their story and the impact their work has on the community. Repometer aims to supplement existing capabilities by collecting timely and insightful data from GitHub and GitLab repositories and passing it to a database for longer-term storage. 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.

Mundt, Miranda↗
DOE OSTI2026

AnnualReportingWind [SWR-26-026]

AnnualReportingWind is a version-controlled repository used to generate the cost and performance results published in major wind energy reports such as the Cost of Wind Energy Review (COWER) and the Annual Technology Baseline (ATB). The repository consolidates the model configurations, assumptions, and scripts used in each reporting year so that published results can be transparently reproduced and traced back to the exact analytical setup used in the analysis. The workflows rely on several techno-economic modeling tools developed at the National Laboratory of the Rockies (NLR), including WAVES, ORBIT, LandBOSSE, WOMBAT, and FLORIS.

Mulas Hernando, Daniel [National Laboratory of the↗