Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Open source software”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Subnanogram proteomics: Impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples

One of the greatest challenges for mass spectrometry (MS)-based proteomics is the limited ability to analyze small samples. Here we investigate the relative contributions of liquid chromatography (LC), MS instrumentation and data analysis methods with the aim of improving proteome coverage for sample sizes ranging from 0.5 ng to 50 ng. We show that the LC separations utilizing 30-µm-i.d. columns increase signal intensity by >3-fold relative to those using 75-µm-i.d. columns, leading to 32% increase in peptide identifications. The Orbitrap Fusion Lumos mass spectrometer significantly boosted both sensitivity and sequencing speed relative to earlier generation Orbitraps (e.g., LTQ-Orbitrap), leading to a ~3× increase in peptide identifications and 1.7× increase in identified protein groups for 2 ng tryptic digests of bacterial lysate. The Match Between Runs algorithm of open-source MaxQuant software further increased proteome coverage by ~ 95% for 0.5 ng samples and by ~42% for 2 ng samples. The present platform is capable of identifying >3000 protein groups from tryptic digestion of cell lysates equivalent to 50 HeLa cells and 100 THP-1 cells (~10 ng total proteins), respectively, and >950 proteins from subnanogram bacterial and archaeal cell lysates. The present ultrasensitive LC-MS platform is expected to enable deep proteome coverage for subnanogram samples, including single mammalian cells.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2020

Three-Dimensional CFD Analysis of Construction Design Alternatives for an ERDC Coastal and Hydraulics Laboratory Flow Accelerator

The U.S. Army Engineer Research and Development Center, ERDC, Coastal and Hydraulics Laboratory in Vicksburg Mississippi is planning to build a large flume with a 10-foot-wide flow channel. Three-dimensional Computational Fluid Dynamics (CFD) analysis was used in the design of the flume entry and flow accelerator sections that feed into the 10-foot-wide channel. The design is based on the plans of the existing fiberglass flume inlet at the Turner-Fairbank Highway Research Center (TFHRC) J. Sterling Jones Hydraulics Research Laboratory in McLean Virginia. The TFHRC flume inlet feeds water to a 6-foot-wide flume channel, and therefore a scale up factor of 10/6 in the width of the inlet section of the TFHRC flume would meet the width requirement of the ERDC flume channel. The CFD analysis was performed using STAR-CCM+ commercial CFD software. Additional analysis was done with the open-source CFD software, OpenFOAM, to cross-check the analysis of one of the cases with a code-to-code comparison.

42 ENGINEERING↗
DOE OSTI2021

Hands-on with OWL: the Oak–Ridge Wang–Landau Monte Carlo software suite

The Oak–Ridge Wang–Landau (OWL) package is an open-source scientific software specialized for large-scale, Monte Carlo simulations for the study of materials properties at finite temperature. In this paper, we discuss the main features and capabilities of OWL, followed by detailed descriptions of building and running the code. The readers will be guided through the usage and functionality of the code with a few hands-on examples. This paper is based on a tutorial on OWL given at the 32nd Center for Simulational Physics Workshop on Recent Developments in Computer Simulation Studies in Condensed Matter Physics.

Li, Ying Wai↗
DOE OSTI2023

Impact of Rubin Observatory Cadence Choices on Supernovae Photometric Classification

The Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) will discover an unprecedented number of supernovae (SNe), making spectroscopic classification for all the events infeasible. LSST will thus rely on photometric classification, whose accuracy depends on the not-yet-finalized LSST observing strategy. In this work, we analyze the impact of cadence choices on classification performance using simulated multiband light curves. First, we simulate SNe with an LSST baseline cadence, a nonrolling cadence, and a presto-color cadence, which observes each sky location three times per night instead of twice. Each simulated data set includes a spectroscopically confirmed training set, which we augment to be representative of the test set as part of the classification pipeline. Then we use the photometric transient classification library snmachine to build classifiers. We find that the active region of the rolling cadence used in the baseline observing strategy yields a 25% improvement in classification performance relative to the background region. This improvement in performance in the actively rolling region is also associated with an increase of up to a factor of 2.7 in the number of cosmologically useful Type Ia SNe relative to the background region. However, adding a third visit per night as implemented in presto-color degrades classification performance due to more irregularly sampled light curves. Overall, our results establish desiderata on the observing cadence related to classification of full SNe light curves, which in turn impacts photometric SNe cosmology with LSST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

A Standardized Analysis Process Using Digital Image Correlation to Calculate In Situ Cladding Strain from Modified Burst Tests for Fuel Performance Code Validation

Historical data collection on nuclear fuel cladding materials has focused on generating a statistically significant amount of data to assess the material and its failure behavior. Furthermore, data generated to support material model and failure criteria development were previously posttest evaluations, so a large number of tests was required to gain new understanding. A way to expedite this process is to develop techniques capable of generating large, high-fidelity data sets from a single test with lower uncertainty or quantified uncertainty. One such example of this approach is Oak Ridge National Laboratory’s use of modified burst tests (MBTs) to analyze the mechanical behavior and failure conditions of cladding during a simulated reactivity-initiated accident (RIA). Each test incorporates digital image correlation (DIC) analysis techniques that are used to assess the accumulated strain in situ, as well as eventual cladding failure. This work has been fruitful in defining strain-to-failure conditions for materials like silicon carbide (SiC) fiber–reinforced/SiC matrix composite tubes (SiC/SiC), iron-chromium-aluminum (FeCrAl) alloy tubes, and chromium-coated Zircaloy-4 tubes. However, there are numerous DIC software available, including open-source and proprietary software. The different DIC software use various algorithms to process images and calculate displacement values. Using these different software and algorithms can lead to varying results, and perhaps larger-than-expected uncertainties. In the present study, previously published MBT data encompassing a variety of test conditions were reanalyzed with two different DIC software to assess the variance in the calculated strain results. The data consisted of SiC/SiC, FeCrAl, and chromium-coated Zircaloy-4 tubes. Plots of the calculated strains during the transient revealed good agreement between the two DIC software. The average root-mean-square errors between the two software was 0.20% strain, which is slightly larger than a previously reported error value for these tests. In conclusion, this variance in results is low enough that this analysis method can be used for code validation.

Reactivity-initiated accident↗
DOE OSTI2024

MCM (Marine Carbon Management) [SWR-24-122]

The marine carbon management software is an open-source Python based software that contains generic models for marine carbon capture, marine carbon dioxide removal, marine carbon capture and utilization, marine carbon capture and storage. The models include design parameters, operational conditions and scenarios and technology costs.

Niffenegger, James↗
DOE OSTI2022

Considerations for Optimizing the Photometric Classification of Supernovae from the Rubin Observatory

The Vera C. Rubin Observatory will increase the number of observed supernovae (SNe) by an order of magnitude; however, it is impossible to spectroscopically confirm the class for all SNe discovered. Thus, photometric classification is crucial, but its accuracy depends on the not-yet-finalized observing strategy of Rubin Observatory's Legacy Survey of Space and Time (LSST). We quantitatively analyze the impact of the LSST observing strategy on SNe classification using simulated multiband light curves from the Photometric LSST Astronomical Time-Series Classification Challenge (PLAsTiCC). First, we augment the simulated training set to be representative of the photometric redshift distribution per SNe class, the cadence of observations, and the flux uncertainty distribution of the test set. Then we build a classifier using the photometric transient classification library snmachine, based on wavelet features obtained from Gaussian process fits, yielding a similar performance to the winning PLAsTiCC entry. We study the classification performance for SNe with different properties within a single simulated observing strategy. We find that season length is important, with light curves of 150 days yielding the highest performance. Cadence also has an important impact on SNe classification; events with median inter-night gap <3.5 days yield higher classification performance. Interestingly, we find that large gaps (>10 days) in light-curve observations do not impact performance if sufficient observations are available on either side, due to the effectiveness of the Gaussian process interpolation. This analysis is the first exploration of the impact of observing strategy on photometric SN classification with LSST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

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↗
DOE OSTI2017

Dakota Technical Support Demonstrations and Software Improvements

Caterpillar, Inc. (Caterpillar) and Sandia National Laboratories (SNL) continued their partnership to improve SNL's open source Dakota software product and effectively deploy it to Caterpillar engineering design and analysis problems. Several new features that are expected to benefit not only Caterpillar but also the entire Dakota user community were introduced. In addition, SNL and Caterpillar cooperated extensively to conduct a demonstration of Dakota's uncertainty quantification capabilities on a computational simulation of relevance to Caterpillar.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Graph-based machine learning improves just-in-time defect prediction

The increasing complexity of today’s software requires the contribution of thousands of developers. This complex collaboration structure makes developers more likely to introduce defect-prone changes that lead to software faults. Determining when these defect-prone changes are introduced has proven challenging, and using traditional machine learning (ML) methods to make these determinations seems to have reached a plateau. In this work, we build contribution graphs consisting of developers and source files to capture the nuanced complexity of changes required to build software. By leveraging these contribution graphs, our research shows the potential of using graph-based ML to improve Just-In-Time (JIT) defect prediction. We hypothesize that features extracted from the contribution graphs may be better predictors of defect-prone changes than intrinsic features derived from software characteristics. We corroborate our hypothesis using graph-based ML for classifying edges that represent defect-prone changes. This new framing of the JIT defect prediction problem leads to remarkably better results. We test our approach on 14 open-source projects and show that our best model can predict whether or not a code change will lead to a defect with an F1 score as high as 77.55% and a Matthews correlation coefficient (MCC) as high as 53.16%. This represents a 152% higher F1 score and a 3% higher MCC over the state-of-the-art JIT defect prediction. We describe limitations, open challenges, and how this method can be used for operational JIT defect prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Alfalfa Virtual Building Service: Software Engineering Best Practices Applied to Runtime Interaction with Building Energy Models

Buildings are active participants in increasingly complex energy systems. Building Energy Modeling (BEM) has a key role to play in planning and de-risking an equitable energy transition, with BEM-backed "virtual buildings" critical path for diverse applications that include workforce training tools, Hardware-in-the-Loop (HIL) experimentation to study equipment performance under a range of conditions, Control-Hardware-in-the-Loop (CHIL) experimentation to de-risk commercial control implementations at equipment through grid orchestration levels, and integration of dynamic load profiles into grid modeling tools for energy system experimentation at the urban scale. Modeling requirements vary across these applications, but many software engineering tasks do not. The Alfalfa Virtual Building Service (AVBS, see https://github.com/NREL/alfalfa/wiki) is an open-source web service that solves these common tasks robustly in one place, providing a foundational platform for power users to bootstrap their own applications. AVBS abstracts the specifics of runtime interaction with OpenStudio, Modelica, and Spawn of EnergyPlus models behind a unified REST API. Additionally, AVBS provides resources for cloud deployment and scaling to 100s of parallel simulations, a growing library of modular Operational Technology (OT) integrations for emulation of real-world interfaces, and scripts to automate the population of communities of virtual buildings from URBANopt, ResStock and ComStock.

building automation↗
DOE OSTI2020

Modeling a ring magnet in ALEGRA

We show here that Sandia's ALEGRA software can be used to model a permanent magnet in 2D and 3D, with accuracy matching that of the open-source commercial software FEMM. This is done by conducting simulations and experimental measurements for a commercial-grade N42 neodymium alloy ring magnet with a measured magnetic field strength of approximately 0.4 T in its immediate vicinity. Transient simulations using ALEGRA and static simulations using FEMM are conducted. Comparisons are made between simulations and measurements, and amongst the simulations, for sample locations in the steady-state magnetic field. The comparisons show that all models capture the data to within 7%. The FEMM and ALEGRA results agree to within approximately 2%. The most accurate solutions in ALEGRA are obtained using quadrilateral or hexahedral elements. In the case where iron shielding disks are included in the magnetized space, ALEGRA simulations are considerably more expensive because of the increased magnetic diffusion time, but FEMM and ALEGRA results are still in agreement. The magnetic field data are portable to other software interfaces using the Exodus file format.

36 MATERIALS SCIENCE↗
DOE OSTI2017

progressbar2

New contributions to the existing open source project called 'progressbars2." Improvements were created for use in JBEI software, but are generally useful to the open source software community.

Forrer, Mark↗
DOE OSTI2017

progressbar2

New contributions to the existing open source project called 'progressbars2." Improvements were created for use in JBEI software, but are generally useful to the open source software community.

Forrer, Mark↗
DOE OSTI2018

Scanning A uger spectromicroscopy using the S cope F oundry software platform

We have developed an open‐source, Python‐based software platform called ScopeFoundry for performing complex, multidimensional microscopy experiments that integrate diverse types of experimental hardware. ScopeFoundry streamlines experiment development by providing a modular environment where hardware controls and measurement schemes can be arranged and customized. Important software tasks such as data management and user interface generation are automated. Using this platform, we have implemented scanning Auger spectromicroscopy on a modified commercial surface analysis system. Spectromicroscopy produces multidimensional datasets with complete spectra at each image pixel, allowing for detailed analysis of material phases where Auger peaks may change in shape and position. Analysis of the surface phases of an advanced electron emission dispenser cathode is presented as an example. We describe the general ScopeFoundry platform, its application to Auger spectromicroscopy, and ways it can be applied to advance surface analysis and microscopy.

Durham, Daniel B.↗
DOE OSTI2017

Modeling Chemical Evolution of Cement Seals

The prevention of the migration of fluids is a field of study with high demand in both the private industry as well as in government research and development. More particularly, the prevention of carbon dioxide (CO 2 ) migration or return to the atmosphere. This, in turn, causes measurably significant atmospheric climate change that results in immense damage to the environment. In this study, the interaction between 0.5 molar sodium chloride (NaCl) brine solution and a cement interface over extended periods of time is computationally investigated, as well as the interaction of a 33 millimolar CO 2 dissolved in the afore-mentioned brine solution for the same period of time. A 2-meter-long saturated brine solution reacted with an 800-meter-long cement block in PFLOTRAN, an open-source reactive flow transport software whose output was later visualized in ParaView, a separate, open-source, visualization software.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗