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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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At least 145 records · Page 8

Programs To Aid FORTRAN Programming

Program-development time decreased while program quality increased. FORTRAN Programming Tools are series of programming tools used to support development and maintenance of FORTRAN 77 source codes. Included are debugging aid, central-processing-unit time-monitoring program, source-code maintenance aids, print utilities, and library of useful, well-documented programs. Tools assist in reducing development time and encouraging high-quality programming. Although intended primarily for FORTRAN programmers, some tools used on data files and other programming languages. Written in FORTRAN 77.

Ragosta, Arthur E.↗

Hydrologic Model Data for the East Fork Poplar Creek Watershed Simulated with the Advanced Terrestrial Simulator (ATS): Streamflow and Network Expansion–Contraction Dynamics

This dataset supports hydrologic modeling and stream network expansion–contraction analysis for the East Fork Poplar Creek (EFPC) Watershed in Tennessee. It includes a Jupyter notebook for model setup, model configuration files, simulation outputs, and derived products used to evaluate model performance and investigate stream dynamics under varying hydrologic conditions. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations using a stream-aligned mesh. Outputs include high-resolution time series of streamflow, active network length, water table depth, and related hydrologic variables. Also included are spatially explicit stream persistency indices and classifications of reaches as perennial or non-perennial. These data facilitate reproducibility and support further research on stream intermittency and variability in network extent.The model data archive is organized in following directories:1) model_setup_inputsContains the Watershed Workflow Jupyter notebooks (accessed through any open source code editor), selected input datasets, and resulting ATS input files, including XML files (access through any open source code editor), computational mesh (.exo files can be viewed using Paraview), and meteorological forcing files (.h5 files can be accessed through h5py python package and HDFView open source software). 2) model_outputsIncludes ATS simulation outputs relevant to this study. Time series of spatially integrated or averaged variables (e.g., streamflow, water table depth) are provided as CSV files. Select spatial fields (e.g., ponded depth and water table depth) are saved as pickled Python objects to reduce file size, and can be accessed through pickle package in Python. Key geometry objects from Watershed Workflow—such as the surface mesh and river tree—are also included to support analysis of streamflow persistency and expansion–contraction dynamics. These files can also be accessed through Watershed Workflow Python package.3) model_evaluationProvides observed streamflow time series and field survey-based flow regime classifications used to evaluate model performance. Jupyter notebooks for processing ATS outputs and comparing model predictions with observations to build confidence in the model prior to scientific analysis are also included.4) Q_L_relationshipsContains workflows for generating time series of discharge, active network length, and related hydrologic variables used in the stream network expansion–contraction analysis. Includes routines for delineating baseflow-dominated periods. For each catchment, notebooks and processed data (as pickled DataFrames accessed through Pandas Python package) are provided. 5) figure_scriptsProvides the Jupyter notebooks used to generate the figures presented in the paper.

54 ENVIRONMENTAL SCIENCES↗

Open Data, Models, and Codes for Vanadium Redox Batch Cell Systems: A Systems Approach Using Zero-Dimensional Models

Abstract In this paper, we study, analyze, and validate some important zero-dimensional physics-based models for vanadium redox batch cell (VRBC) systems and formulate an adequate physics-based model that can predict the battery performance accurately. In the model formulation process, a systems approach to multiple parameters estimation has been conducted using VRBC systems at low C-rates (~C/30). In this batch cell system, the effect of ions' crossover through the membrane is dominant, and therefore, the capacity loss phenomena can be explicitly observed. Paradoxically, this means that using the batch system might be a better approach for identifying a more suitable model describing the effect of ions transport. Next, we propose an efficient systems approach, which enables to help understand the battery performance quickly by estimating all parameters of the battery system. Finally, open source codes, executable files, and experimental data are provided to enable people's access to robust and accurate models and optimizers. In battery simulations, different models and optimizers describing the same systems produce different values of the estimated parameters. Providing an open access platform can accelerate the process to arrive at robust models and optimizers by continuous modification from the users' side.

25 ENERGY STORAGE↗

Versatile Dual-Channel Waveform Generator

Programmable waveform generator synthesizes two independent waveforms simultaneously at frequencies up to 250 MHz. Can be in phase or out of phase with each other. Use of commercial integrated circuits helps keep cost low. Operation governed by BASIC source code enabling any user equipped with suitable personal computer to specify waveforms. User can modify source code to satisfy special needs. Other applications include simulation of Doppler waveforms for radar, and of video signals for testing color displays and computer monitors. With eventual substitution of gallium arsenide integrated circuits for its present silicon integrated circuits, instrument able to generate waveforms with 14-bit precision and sample rates as high as 2 GHz.

Staples, Edward J.↗

CTF 4.0 Theory Manual

Coolant-Boiling in Rod Arrays - Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e., fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of 9 conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently re-branded as CTF. As part of the improvement process, it was necessary to generate sufficient documentation for the open-source code which had lacked such material upon being adopted by RDFMG. This document serves mainly as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code as well as the numerical solution process utilized. Coding of the models is also discussed, all with consideration for updates that have been made when transitioning from COBRA-TF to CTF. Further documentation outside of this manual is also available at RDFMG which focus on code input deck generation and source code global variable and module listings.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

CTF Theory Manual (V.4.2)

Coolant-Boiling in Rod Arrays—Two Fluids (COBRA-TF) is a thermal/hydraulic (T/H) simulation code designed for light water reactor (LWR) vessel analysis. It uses a two-fluid, three-field (i.e. fluid film, fluid drops, and vapor) modeling approach. Both sub-channel and 3D Cartesian forms of 9 conservation equations are available for LWR modeling. The code was originally developed by Pacific Northwest Laboratory in 1980 and had been used and modified by several institutions over the last few decades. COBRA-TF also found use at the Pennsylvania State University (PSU) by the Reactor Dynamics and Fuel Modeling Group (RDFMG) and has been improved, updated, and subsequently re-branded as CTF. As part of the improvement process, it was necessary to generate sufficient documentation for the open-source code which had lacked such material upon being adopted by RDFMG. This document serves mainly as a theory manual for CTF, detailing the many two-phase heat transfer, drag, and important accident scenario models contained in the code as well as the numerical solution process utilized. Coding of the models is also discussed, all with consideration for updates that have been made when transitioning from COBRA-TF to CTF. Further documentation outside of this manual is also available at RDFMG which focus on code input deck generation and source code global variable and module listings

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association

Abstract Motivation Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Supplementary information Supplementary data are available at Bioinformatics online.

Ma, Jian↗

Unified Language Frontend for Physic-Informed AI/ML

Artificial intelligence and machine learning (AI/ML) are becoming important tools for scientific modeling and simulation as in several other fields such as image analysis and natural language processing. ML techniques can leverage the computing power available in modern systems and reduce the human effort needed to configure experiments, interpret and visualize results, draw conclusions from huge quantities of raw data, and build surrogates for physics based models. Domain scientists in fields like fluid dynamics, microelectronics and chemistry can automate many of their most difficult and repetitive tasks or improve the design times by use of the faster ML-surrogates. However, modern ML and traditional scientific highperformance computing (HPC) tend to use completely different software ecosystems. While ML frameworks like PyTorch and TensorFlow provide Python APIs, most HPC applications and libraries are written in C++. Direct interoperability between the two languages is possible but is tedious and error-prone. In this work, we show that a compiler-based approach can bridge the gap between ML frameworks and scientific software with less developer effort and better efficiency. We use the MLIR (multi-level intermediate representation) ecosystem to compile a pre-trained convolutional neural network (CNN) in PyTorch to freestanding C++ source code in the Kokkos programming model. Kokkos is a programming model widely used in HPC to write portable, shared-memory parallel code that can natively target a variety of CPU and GPU architectures. Our compiler-generated source code can be directly integrated into any Kokkosbased application with no dependencies on Python or cross-language interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Terminal Area Simulation System User's Guide - Version 10.0

The Terminal Area Simulation System (TASS) is a three-dimensional, time-dependent, large eddy simulation model that has been developed for studies of wake vortex and weather hazards to aviation, along with other atmospheric turbulence, and cloud-scale weather phenomenology. This document describes the source code for TASS version 10.0 and provides users with needed documentation to run the model. The source code is programed in Fortran language and is formulated to take advantage of vector and efficient multi-processor scaling for execution on massively-parallel supercomputer clusters. The code contains different initialization modules allowing the study of aircraft wake vortex interaction with the atmosphere and ground, atmospheric turbulence, atmospheric boundary layers, precipitating convective clouds, hail storms, gust fronts, microburst windshear, supercell and mesoscale convective systems, tornadic storms, and ring vortices. The model is able to operate in either two- or three-dimensions with equations numerically formulated on a Cartesian grid. The primary output from the TASS is time-dependent domain fields generated by the prognostic equations and diagnosed variables. This document will enable a user to understand the general logic of TASS, and will show how to configure and initialize the model domain. Also described are the formats of the input and output files, as well as the parameters that control the input and output.

Switzer, George F.↗

Extension of mutation testing for the requirements and design faults - 322

Mutation Testing is a fault-based software testing technique that is considered to be the most efficient in detecting faults. It focuses on the software code level and follows a set of rules which are called mutation operators to systematically seed faults into the source code. Each seeded fault results is a new version of the software, which is called a mutant. Mutation testing promises to be effective in identifying adequate test data which can be used to find faults in the source code. However, traditional mutation testing is not geared towards the detection of requirements and design faults. To cover the full spectrum of possible faults, the mutation framework has been extended from the code level to the requirements and design level. Twenty-nine defects that appear in requirements and design documents were identified to define appropriate mutants. Then corresponding mutation operators that model the defects were developed. For each mutation operator, the strategy to generate a mutant and the evaluation of the number of possible mutants were defined. Existing code level cost reduction techniques were tailored for requirements and design mutation operators that result in a large number of mutants. With the extended mutation testing framework, the full spectrum of possible faults will be tested and identified to ensure the safety and functionality of the software. (authors)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

ECP Milestone Memo WBS 2.3.4.13 ECP/VTK-m FY19Q1 [MS-19/01-03] ZFP / Release / Clip STDA05-17

The STDA05-17 milestone comprises the following 3 deliverables. VTK-m Release 2 We will provide a release of VTK-m software and associated documentation. The source code repository will be tagged at a stable state, and, at a minimum, tarball captures of the source code will be made available from the web site. A version of the VTK-m User's Guide documenting this release will also be made available. Productionize zfp compression The "ZFP: Compressed Floating-Point Arrays" project (WBS 1.3.4.13) is creating an implementation of ZFP compression in VTK-m. Their implementation will be focused on operating in CUDA. The VTK-m project will assist by generalizing the implementation to other devices (such as multi-core CPUs). We will also assist in productionizing the code such that it can be used by external projects and products. Clip Clip operations intersect meshes with implicit functions. It is the foundation of spatial subsetting algorithms, such as "box," and the foundation of data-based subsetting, such as "isovolume." The algorithm requires considering thousands of possible cases, and is thus quite difficult to implement. This milestone will implement clipping to be sufficient for Visit's and ParaView's needs.

97 MATHEMATICS AND COMPUTING↗

Software engineering capability for Ada (GRASP/Ada Tool)

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD). The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada PDL or source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada Source code. A new Motif compliant graphical user interface has been developed for the GRASP/Ada prototype.

Cross, James H., II↗

Using CAASCADE and CrayPAT for Analysis of HPC Applications

We describe our work on integrating CAASCADE with CrayPAT to obtain both static and dynamic information on characteristics of high-performance computing (HPC) applications. CAASCADE --- Compiler-Assisted Application Source Code Analysis and Database---is a system we are developing to extract features of application from its source code by utilizing compiler plugins. CrayPAT enable us to add runtime-based information to CAASCADE's feature detection. We present results from analysis of HPC applications.

Budiardja, Reuben↗

MCNP6 and SERPENT2 Performances with Unstructured Mesh Geometry

Traditionally, Monte Carlo codes model a nuclear reactor by combinatorial geometry. In this model, volume primitives (e,g, spheres, cylinders, parallelepipeds...) are combined together by Boolean operations (e.g. union, intersection, and complement) and replicated by lattice definitions to build the core geometry. Recently, high performances computing platforms allowed using unstructured mesh geometry in Monte Carlo codes. When this option is chosen, any type of core geometry can be modeled since the restriction of using volume primitives is removed. In an unstructured mesh geometry, Boolean operations and lattice definitions are not used since each volume is defined by triangular surfaces (facets). This study focuses on two Monte Carlo codes: MCNP (version 6.1.1 beta) developed at Los Alamos National Laboratory since 1957 and written in FORTRAN90, C, and C++ (267,000 total source code lines), and SERPENT (version 2.1.27) developed at VTT Technical Research Centre since 2004 and written in C (195,000 total source code lines). These two codes follow different approaches for the unstructured mesh geometry modeling: MCNP uses ABAQUS format, whereas SERPENT uses the STL format. In the STL (STereoLithographic) geometry model only the surfaces of the volume are meshed; the interior part of the volumes is not meshed. In the STL geometry model, the whole geometry is defined by the sequence of SOLID and ENDSOLID sections. Each volume of the geometry must have a SOLID and ENDSOLID section. The STL file contains no information specifying the materials of the volumes. MCNP and SERPENT can model any kind of complicated geometry using unstructured meshes. MCNP and SERPENT use the ABAQUS and STL file formats, respectively. The STL file format does not have tetrahedrons and has only triangular facets on the volumes boundary. This allows SERPENT simulations to run 10 times faster than MCNP. However, if Monte Carlo results have to be coupled to thermal-hydraulics codes, the interior of the geometry volumes must be meshed, which may reduce SERPENT performances.

97 MATHEMATICS AND COMPUTING↗

Advances in data compression

A rigorous real-variables treatment of general data compression and encoding problems, centered on formulation and proof of relevant existence theorems and a unified formulation of source coding (both noiseless and with a fidelity criterion) in inaccurately or incompletely specified statistical environments. Difficulties in modeling of sources with unknown or imperfectly known statistical descriptions are analyzed and source codes (SC) are classified (variable-rate noiseless SC, fixed-rate noiseless SC) and analyzed, along with types of code sequences (weighted-universal, maximin-universal, strongly or weakly minimax-universal). Universal coding on video data, variable-rate coding with distortion, and distortion-rate functions are discussed. Design strategies for universal coding algorithms are suggested, but the article is not oriented to specific methods of synthesizing data compression systems.

Davisson, L. D.↗

Support for Systematic Code Reviews with the SCRUB Tool

SCRUB is a code review tool that supports both large, team-based software development efforts (e.g., for mission software) as well as individual tasks. The tool was developed at JPL to support a new, streamlined code review process that combines human-generated review reports with program-generated review reports from a customizable range of state-of-the-art source code analyzers. The leading commercial tools include Codesonar, Coverity, and Klocwork, each of which can achieve a reasonably low rate of false-positives in the warnings that they generate. The time required to analyze code with these tools can vary greatly. In each case, however, the tools produce results that would be difficult to realize with human code inspections alone. There is little overlap in the results produced by the different analyzers, and each analyzer used generally increases the effectiveness of the overall effort. The SCRUB tool allows all reports to be accessed through a single, uniform interface (see figure) that facilitates brows ing code and reports. Improvements over existing software include significant simplification, and leveraging of a range of commercial, static source code analyzers in a single, uniform framework. The tool runs as a small stand-alone application, avoiding the security problems related to tools based on Web browsers. A developer or reviewer, for instance, must have already obtained access rights to a code base before that code can be browsed and reviewed with the SCRUB tool. The tool cannot open any files or folders to which the user does not already have access. This means that the tool does not need to enforce or administer any additional security policies. The analysis results presented through the SCRUB tool s user interface are always computed off-line, given that, especially for larger projects, this computation can take longer than appropriate for interactive tool use. The recommended code review process that is supported by the SCRUB tool consists of three phases: Code Review, Developer Response, and Closeout Resolution. In the Code Review phase, all tool-based analysis reports are generated, and specific comments from expert code reviewers are entered into the SCRUB tool. In the second phase, Developer Response, the developer is asked to respond to each comment and tool-report that was produced, either agreeing or disagreeing to provide a fix that addresses the issue that was raised. In the third phase, Closeout Resolution, all disagreements are discussed in a meeting of all parties involved, and a resolution is made for all disagreements. The first two phases generally take one week each, and the third phase is concluded in a single closeout meeting.

Holzmann, Gerald J.↗

ECP ST Project 2.3.1.06-STPM08-RAJA (Final Report)

Modern high-performance computing architectures are diverse, with hardware designs that feature multicore CPUs and CPUs plus accelerators, such as GPUs or FPGAs. Achieving good application performance often requires using a programming model and managing application data in ways that are best suited to a particular platform. For large codes that are used daily in production, and are under continual development, architecture-specific ports are untenable. Maintainability requires single-source code that is performance portable across a range of architectures and programming model back-ends. This report describes RAJA, Umpire, and CHAI, three software libraries that provide complementary capabilities to enable application portability for high performance computing (HPC) platforms. In particular, these libraries provide software abstractions that insulate application source code from hardware architecture and programming model-specific implementation details. These development of these libraries was motivated by the needs of multiphysics applications in the Weapons Simulation and Computing Program (WSC) at Lawrence Livermore National Laboratory (LLNL). Funding though the Exascale Computing Project (ECP) Software Technology (ST) project 2.3.1.06 RAJA has fostered outreach and collaboration with the ECP application and software technology development communities. In this report, we describe ECP adoption and integration of these tools to this point. The larger goal of the report is to describe to the ECP community what these projects offer, how they are used, and how to approach adoption and integration of them.

97 MATHEMATICS AND COMPUTING↗

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

MOTIVATION: High-throughput sequencing (HTS) is a modern sequencing technology used to profile microbiomes by sequencing thousands of short genomic fragments from the microorganisms within a given sample. This technology presents a unique opportunity for artificial intelligence to comprehend the underlying functional relationships of microbial communities. However, due to the unstructured nature of HTS data, nearly all computational models are limited to processing DNA sequences individually. This limitation causes them to miss out on key interactions between microorganisms, significantly hindering our understanding of how these interactions influence the microbial communities as a whole. Furthermore, most computational methods rely on post-processing of samples which could inadvertently introduce unintentional protocol-specific bias. RESULTS: Addressing these concerns, we present SetBERT, a robust pre-training methodology for creating generalized deep learning models for processing HTS data to produce contextualized embeddings and be fine-tuned for downstream tasks with explainable predictions. By leveraging sequence interactions, we show that SetBERT significantly outperforms other models in taxonomic classification with genus-level classification accuracy of 95%. Furthermore, we demonstrate that SetBERT is able to accurately explain its predictions autonomously by confirming the biological-relevance of taxa identified by the model. AVAILABILITY AND IMPLEMENTATION: All source code is available at https://github.com/DLii-Research/setbert. SetBERT may be used through the q2-deepdna QIIME 2 plugin whose source code is available at https://github.com/DLii-Research/q2-deepdna.

Ludwig, David W↗