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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Water Network Tool for Resilience Version 0.1

Water utilities are vulnerable to a wide variety of human-caused and natural disasters. These disruptive events can result in loss of water service, contaminated water, pipe breaks, and failed equipment. Furthermore, long term changes in water supply and customer demand can have a large impact on the operating conditions of the network. The ability to maintain drinking water service during and following these types of events is critical. Simulation and analysis tools can help water utilities explore how their network will respond to disruptive events and plan effective mitigation strategies. The U.S. Environmental Protection Agency and Sandia National Laboratories are developing new software tools to meet this need. The Water Network Tool for Resilience (WNTR, pronounced winter) is a Python package designed to help water utilities investigate resilience of water distribution systems over a wide range of hazardous scenarios and to evaluate resilience-enhancing actions. The following documentation includes installation instructions and examples, description of software features, and software license. It is assumed that the reader is familiar with the Python Programming Language.

42 ENGINEERING↗
DOE OSTI2019

Hanford Surface Barrier Design Guidance

This status report presents results of progress made during fiscal year 2019 towards developing a software tool for designing surface barriers in the Central Plateau. This tool is intended to be used to support feasibility studies and remedy applications. This status report summarizes the methodology followed to develop preliminary vadose zone reduced order models (VZ-ROMs) for use in such a tool. The ROM development process required generation of a training and testing dataset representing an example waste site in the Central Plateau. This training data was prepared via eSTOMP simulations that simulated variable drainage through hypothetical surface barriers into waste sites within the Central Plateau. Prior to regression analysis, these numerical results were analyzed to understand the behavior of contaminant solutes under different drainage conditions in the vadose zone. Results from eSTOMP simulations provided an understanding of the effectiveness of hypothetical surface barriers in isolating the subsurface system and mitigating contaminant transport. The primary objective of the work was to establish an appropriate ROM methodology. Further development is required to adapt the ROMs presented here to appropriately couple surface barrier construction design. Future iterations will be used to predict the performance of different surface barrier engineering designs. Future development will follow a similar process to the one demonstrated in this document.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

SU-F-BRB-07: A Plan Comparison Tool to Ensure Robustness and Deliverability in Online-Adaptive Radiotherapy

Purpose: To develop a plan comparison tool that will ensure robustness and deliverability through analysis of baseline and online-adaptive radiotherapy plans using similarity metrics. Methods: The ViewRay MRIdian treatment planning system allows export of a plan file that contains plan and delivery information. A software tool was developed to read and compare two plans, providing information and metrics to assess their similarity. In addition to performing direct comparisons (e.g. demographics, ROI volumes, number of segments, total beam-on time), the tool computes and presents histograms of derived metrics (e.g. step-and-shoot segment field sizes, segment average leaf gaps). Such metrics were investigated for their ability to predict that an online-adapted plan reasonably similar to a baseline plan where deliverability has already been established. Results: In the realm of online-adaptive planning, comparing ROI volumes offers a sanity check to verify observations found during contouring. Beyond ROI analysis, it has been found that simply editing contours and re-optimizing to adapt treatment can produce a delivery that is substantially different than the baseline plan (e.g. number of segments increased by 31%), with no changes in optimization parameters and only minor changes in anatomy. Currently the tool can quickly identify large omissions or deviations from baseline expectations. As our online-adaptive patient population increases, we will continue to develop and refine quantitative acceptance criteria for adapted plans and relate them historical delivery QA measurements. Conclusion: The plan comparison tool is in clinical use and reports a wide range of comparison metrics, illustrating key differences between two plans. This independent check is accomplished in seconds and can be performed in parallel to other tasks in the online-adaptive workflow. Current use prevents large planning or delivery errors from occurring, and ongoing refinements will lead to increased assurance of plan quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Monitoring and Repair of Cement-Geomaterial Interfaces in Borehole and Repository Scenarios

The failure of subsurface seals (i.e., wellbores, shaft and drift seals in a deep geologic nuclear waste repository) has important implications for US Energy Security. The performance of these cementitious seals is controlled by a combination of chemical and mechanical forces, which are coupled processes that occur over multiple length scales. The goal of this work is to improve fundamental understanding of cement-geomaterial interfaces and develop tools and methodologies to characterize and predict performance of subsurface seals. This project utilized a combined experimental and modeling approach to better understand failure at cement-geomaterial interfaces. Cutting-edge experimental methods and characterization methods were used to understand evolution of the material properties during chemo-mechanical alteration of cement-geomaterial interfaces. Software tools were developed to model chemo-mechanical coupling and predict the complex interplay between reactive transport and solid mechanics. Novel, fit-for-purpose materials were developed and tested using fundamental understanding of failure processes at cement-geomaterial interfaces.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Overview of the OECD-NEA Working Party on International Nuclear Data Evaluation Cooperation (WPEC)

The OECD Nuclear Energy Agency (NEA) Working Party on International Nuclear Data Evaluation Cooperation (WPEC) was established in 1989 to facilitate collaboration in nuclear data activities. Over its thirty year history, different Subgroups have been created to address topics in nearly every aspect of nuclear data, including: experimental measurements, evaluation, validation, model development, quality assurance of databases and the development of software tools. WPEC has recently completed activities on fission yield evaluation, the general nuclear database structure (GNDS) to replace the ENDF-6 format, methods to provide feedback to evaluation, studies of specific capture cross sections, new methods in thermal scattering kernel evaluation and the Collaborative International Evaluated Library Organisation (CIELO) Pilot Project. Ongoing activities in GNDS application programming interface (API) development, methods for covariance evaluation and quality assurance in nuclear data validation using the International Criticality Safety Benchmark Evaluation Project (ICSBEP) database are complemented by the work of two Expert Groups that oversee the High-Priority Request List (HPRL) for Nuclear Data and the continuous development of the GNDS. New activities on the use of integral experiments for nuclear data validation and adjustment, as well as the use of the Shielding Integral Benchmark Archive and Database (SINBAD) for validation have begun and will be coordinated alongside future Subgroups. After three decades we will review the status of WPEC, how it integrates other collections and activities organised by the NEA and how it dovetails with the initiatives of the IAEA and other bodies to effectively coordinate international activities in nuclear data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Software for Tool Design and Testing

Abstract—: The development of software for calculating the cutting parameters in the course of machining or in simulations is discussed. The software developed may be used to create and test new cutting tools.

42 ENGINEERING↗
DOE OSTI2023

Developing Ultrahigh-Resolution E3SM Land Model for GPU Systems

Designing and refactoring complex scientific code, such as the E3SM land model (ELM), for new computing architectures is challenging. This paper presents design strategies and technical approaches to develop a data-oriented, GPU-ready ELM model using compiler directives (OpenACC/OpenMP). We first analyze the datatypes and processes in the original ELM code. Then we present design considerations for ultrahigh-resolution ELM (uELM) development for massive GPU systems. These techniques include the global data-oriented simulation workflow, domain partition, code porting and data copy, memory reduction, parallel loop restructure and flattening, and race condition detection. We implemented the first version of uELM using OpenACC targeting the NVidia GPUs in the Summit supercomputer at Oak Ridge National Laboratory. During the implementation, we developed a software tool (named SPEL) to facilitate code generation, verification, and performance tuning using these techniques. The first uELM implementation for Nvidia GPUs on Summit delivered promising results: 1) over 98% of the ELM code was automatically generated and tuned by scripts. Most ELM modules had better computational performances than the original ELM code for CPUs. The GPU-ready uELM is more scalable than the CPU code on fully-loaded Summit nodes. Example profiling results from several modules are also presented to illustrate the performance improvements and race condition detection. The lessons learned and toolkit developed in the study are also suitable for further uELM deployment using OpenMP on the first US exascale computer, Frontier, equipped with AMD CPUs and GPUs.

Schwartz, Peter↗
DOE OSTI2016

Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D 1 H NMR/ESI MS 1 approach: Hybrid 1D 1 H NMR/ESI MS 1 metabolomics method

We present a novel approach to improve accuracy of metabolite identification by combining direct infusion ESI MS1 with 1D 1H NMR spectroscopy. The new approach first applies standard 1D 1H NMR metabolite identification protocol by matching the chemical shift, J-coupling and intensity information of experimental NMR signals against the NMR signals of standard metabolites in metabolomics library. This generates a list of candidate metabolites. The list contains false positive and ambiguous identifications. Next, we constrained the list with the chemical formulas derived from high-resolution direct infusion ESI MS1 spectrum of the same sample. Detection of the signals of a metabolite both in NMR and MS significantly improves the confidence of identification and eliminates false positive identification. 1D 1H NMR and direct infusion ESI MS1 spectra of a sample can be acquired in parallel in several minutes. This is highly beneficial for rapid and accurate screening of hundreds of samples in high-throughput metabolomics studies. In order to make this approach practical, we developed a software tool, which is integrated to Chenomx NMR Suite. The approach is demonstrated on a model mixture, tomato and Arabidopsis thaliana metabolite extracts, and human urine.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2020

Exploiting Colorimetry for Fidelity in Data Visualization

Advances in multimodal characterization methods fuel the generation of increasing immense hyper-dimensional data sets. Color mapping is employed for conveying higher dimensional data in two-dimensional (2D) representations for human consumption without relying on multiple projections. How one constructs these color maps, however, critically affects how accurately one perceives data. For simple scalar fields, perceptually uniform color maps and color selection have been shown to improve data readability and interpretation across research fields. In this work, we review core concepts underlying the design of perceptually uniform color maps and extend the concepts from scalar fields to two-dimensional vector fields and three-component composition fields frequently found in materials-chemistry research to enable high-fidelity visualization. Additionally, we develop the software tools PAPUC and CMPUC to enable researchers to utilize these colorimetry principles and employ perceptually uniform color spaces for rigorously meaningful color mapping of higher dimensional data representations. Last, we demonstrate how these approaches deliver immediate improvements in data readability and interpretation in microscopies and spectroscopies routinely used in discerning materials structure, chemistry, and properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

SU-D-BRD-01: An Automated Physics Weekly Chart Checking System Supporting ARIA

Purpose: A software tool was developed in this study to perform automatic weekly physics chart check on the patient data in ARIA. The tool accesses the electronic patient data directly from ARIA server and checks the accuracy of treatment deliveries, and generates reports which summarize the delivery history and highlight the errors. Methods: The tool has four modules. 1) The database interface is designed to directly access treatment delivery data from the ARIA database before reorganizing the data into the patient chart tree (PCT). 2) PCT is a core data structure designed to store and organize the data in logical hierarchies, and to be passed among functions. 3) The treatment data check module analyzes the organized data in PCT and stores the checking results into PCT. 4) Report generation module generates reports containing the treatment delivery summary, chart checking results and plots of daily treatment setup parameters (couch table positions, shifts of image guidance). The errors that are found by the tool are highlighted with colors. Results: The weekly check tool has been implemented in MATLAB and clinically tested at two major cancer centers. Javascript, cascading style sheets (CSS) and dynamic HTML were employed to create the user-interactive reports. It takes 0.06 second to search the delivery records of one beam with PCT and compare the delivery records with beam plan. The reports, saved in the HTML files on shared network folder, can be accessed by web browser on computers and mobile devices. Conclusion: The presented weekly check tool is useful to check the electronic patient treatment data in Varian ARIA system. It could be more efficient and reliable than the manually check by physicists. The work was partially supported by a research grant from Varian Medical System.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Automating linear accelerator quality assurance

Purpose: The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers. Methods: The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suite at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs. Results: For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (<0.12 mm) for all Linacs. Considering both log files and EPID measurements, all parameters were well within published tolerance values. Variations in collimator angle, MLC position, and gantry sag were also evaluated for all Linacs. Conclusions: The performance of the TrueBeam Linac model was shown to be consistent based on automated analysis of trajectory log files and EPID images acquired during delivery of a standardized test suite. The results can be compared directly to tolerance thresholds. In addition, sharing of results from standard tests across institutions can facilitate the identification of QA process and Linac changes. These reference values are presented along with the standard deviation for common tests so that the test suite can be used by other centers to evaluate their Linac performance against those in this consortium.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Layer-wise Imaging Dataset from Powder Bed Additive Manufacturing Processes for Machine Learning Applications (Peregrine v2021-03)

This dataset contains layer-wise powder bed images from three different powder bed printing technologies – laser powder bed fusion, electron beam powder bed fusion, and binder jetting. This dataset was collected and annotated using the internally-developed Peregrine software tool and is designed primarily to facilitate research into anomaly defect detection using image segmentation or similar techniques. A total of 20 layers are provided for each printing technology, with each layer of data consisting of one or more calibrated images and an annotation file containing pixel-wise ground truth labels. The ground truths were labeled by domain experts, typically printer technicians. Data in this release were collected at Oak Ridge National Laboratory between 2016 and 2020 and were compiled in March 2021.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Accomplishments of Sandia and Kitware CMake/CTest/CDash Contract for (FY2017-2020)

We describe the accomplishments jointly achieved by Kitware and Sandia over the fiscal years 2016 through 2020 to benefit the Advanced Scientific Computed (ASC) Advanced Technology Development and Mitigation (ATDM) project. As a result of our collaboration, we have improved the Trilinos and ATDM application developer experience by decreasing the time to build, making it easier to identify and resolve build and test defects, and addressing other issues . We have also reduced the turnaround time for continuous integration (CI) results. For example, the combined improvements likely cut the wall clock time to run automated builds of Trilinos posting to CDash by approximately 6x or more in many cases. We primarily achieved these benefits by contributing changes to the Kitware CMake/CTest/CDash suite of open source software development support tools. As a result, ASC developers can now spend more time improving code and less time chasing bugs. And, without this work, one can argue that the stabilization of Trilinos for the ATDM platforms would not have been feasible which would have had a large negative impact on an important internal FY20 L1 milestone.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Science Reach of the SuperCDMS SNOLAB Experiment (Final Report)

The work carried out as part of this project focuses on the development of software tools to calculate the scientific reach of the SuperCDMS dark matter detection experiment, and to enable projection of the potential reach of future experiments base on this technology.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Using Systems Approaches to Improve Photosynthesis and Water Use Efficiency in Sorghum

Throughout the 5 years of this project, 8 labs coordinated to make significant progress on our understanding of how C4 grasses, which include some of our most important crops, can use water more efficiently. We took an integrated approach, using physiology to study how to improve photosynthesis, how to manipulate the pores that move water and CO2 in and out of leaves and the formation and structure of roots. We coupled that with genetic and computational approaches to identify the genes controlling these traits and then used modeling to understand how the genomic system integrates the functions of the genes. We then developed synthetic biology approaches to manipulate the genes and gene editing and plant transformation approaches to insert those traits into a model C4 grass and the bioenergy crop Sorghum bicolor. Through the course of the project, we developed new software tools and genetic resources, filed 5 patents and published 46 papers. We made significant contributions to the bioeconomy through the training of undergraduates, graduate students and postdoctoral researchers. In addition to addressing the specific objectives, our work on this project led to several new and exciting outcomes. We were also to use our expertise and efforts to contribute to many community efforts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

The Release of the Simplified Radionuclide Transport (SRT) Code (V.2.1)

Reactor licensing centers on the protection of the public and environment from the inadvertent release of radioactive material. Therefore, mechanistic source term analysis, or the realistic evaluation of radionuclide transport from the source to the environment for specific transient scenarios, is vital to reactor licensing efforts. Developed to resolve a gap in mechanistic source term modeling capabilities for sodium fast reactors (SFRs), the Simplified Radionuclide Transport (SRT) code created by Argonne National Laboratory (Argonne) is now utilized by advanced reactor vendors, universities, and research institutions to support a multitude of design, licensing, and research efforts. Recently, SRT version 2.1 was released, which includes improvements to code models and verification and validation (V&V) suite to support the SRT user community. The following work provides an overview of the improvements made as part of the release of SRT version 2.1. This effort is supported by the U.S. Department of Energy Office of Nuclear Energy (DOE:NE) Advanced Reactor Technologies (ART) Fast Reactor Program (FRP), as part of the program’s support of national laboratory design and safety analysis computer codes utilized by the fast reactor industry. The expansion of SRT code capabilities and improvements to code V&V associated with version 2.1 are in response to user requests and lessons learned from recent source term analyses performed by Argonne and advanced reactor vendors. They also align with the evolving role of SRT, from research and development tool to software utilized for reactor licensing calculations. The report is structured in alignment with the code improvements, as outlined in Figure 1-1. Section 2 provides background information on SRT, including its history, capabilities, and utilization. Section 3 details new code capabilities as part of version 2.1, while Section 4 focuses on the expansion of the code’s V&V suite. Lastly, Section 5 provides a summary and discussion of next steps.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗