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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 1,135 records · Page 63

LaDa™

High-Throughput software platform to create/launch/analyze physics-related calculations. The front-end is a python API which allows the user to create any conceivable first-principles physics calculation. Is is coupled to an ipython interface to launch and retrieve large number of calculations. It was successfully used in high-throughput calculations of point defect formation enthalpies, compound formation enthalpies, and a genetic algorithm search of direct-gap silicon/germanium structures.

Source record↗

Formularity: Software for Automated Formula Assignment of Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra

Ultrahigh-resolution mass spectrometry, such as Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work we describe a user friendly interface for CIA, titled Formularity, which includes an additional functionality to perform search of formulas based on an Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. The HOC spike in NOM and tap water were used to assess HOC identification in natural and anthropogenic matrices. Strategies for reconciliation of CIA and IPA assignments are discussed. Software and sample databases with documentation are freely available from the PNNL OMICS software repository https://omics.pnl.gov/software/formularity.

data analysis↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Novel functional and distributed approaches to data analysis available in ROOT

The bright future of particle physics at the Energy and Intensity frontiers poses exciting challenges to the scientific software community. The traditional strategies for processing and analyzing data are evolving in order to (i) offer higher-level programming model approaches and (ii) exploit parallelism to cope with the ever increasing complexity and size of the datasets. This contribution describes how the ROOT framework, a cornerstone of software stacks dedicated to particle physics, is preparing to provide adequate solutions for the analysis of large amount of scientific data on parallel architectures. The functional approach to parallel data analysis provided with the ROOT TDataFrame interface is then characterized. The design choices behind this new interface are described also comparing with other widely adopted tools such as Pandas and Apache Spark. The programming model is illustrated highlighting the reduction of boilerplate code, composability of the actions and data transformations as well as the capabilities of dealing with different data sources such as ROOT, JSON, CSV or databases. Details are given about how the functional approach allows transparent implicit parallelization of the chain of operations specified by the user. The progress done in the field of distributed analysis is examined. In particular, the power of the integration of ROOT with Apache Spark via the PyROOT interface is shown. In addition, the building blocks for the expression of parallelism in ROOT are briefly characterized together with the structural changes applied in the building and testing infrastructure which were necessary to put them in production.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Portals Reference Implementation v. 1.0

The Portals reference implementation is based on the Portals 4.X API, published by Sandia National Laboratories as a freely available public document. It is designed to be an implementation of the Portals Networking Application Programming Interface and is used by several other upper layer protocols like SHMEM, GASNet and MPI. It is implemented over existing networks, specifically Ethernet and InfiniBand networks. This implementation provides Portals networks functionality and serves as a software emulation of Portals compliant networking hardware. It can be used to develop software using the Portals API prior to the debut of Portals networking hardware, such as Bull’s BXI interconnect, as well as a substitute for portals hardware on development platforms that do not have Portals compliant hardware. The reference implementation provides new capabilities beyond that of a typical network, namely the ability to have messages matched in hardware in a way compatible with upper layer software such as MPI or SHMEM. It also offers methods of offloading network operations via triggered operations, which can be used to create offloaded collective operations. Specific details on the Portals API can be found at http://portals4.org.

Grant, RyanE.↗

ORNL/grit

Grit is a software library designed specifically for conducting particle-based Lagrangian simulations with CPU/GPUperformance portability. This library allows researchers and engineers to perform a wide range of simulations, including multiphase flow, and more. Grit employs Message Passing Interface (MPI) for distributed memory parallelism and Kokkos programming model for on-node shared memory parallelism with performance portability across different architectures of GPUs and multi-core/manycore CPUs.

Ge, Wenjun [Oak Ridge National Laboratory (ORNL), ↗

Unified differentiable digital twin for the IOTA/FAST facility

As the design complexity of modern accelerators grows, there is more interest in using advanced simulations that have fast execution time or produce insights about accelerator state. One notable example of additional information are gradients of physical observables with respect to design parameters produced by differentiable simulations. The IOTA/FAST facility has recently begun a program to implement and experimentally validate a unified start-to-end differentiable digital twin to serve as a virtual accelerator test stand, allowing for rapid prototyping of new software and experiments with minimal beam time costs. In this contribution we will discuss our plans and progress. Specifically, we will cover the selection and benchmarking of both physics and ML codes, the development of generic interfaces between device models and surrogate or physics-based sections, and the export of the parameters through either a deterministic event loop or a fully asynchronous EPICS soft input/output controller. We will also discuss challenges in model calibration and uncertainty quantification, as well as future plans to support larger proton accelerators like PIPII and Booster.

Kuklev, Nikita [Fermilab]↗

FAST: A Fast Full System Cycle Accurate Computer Simulator (Early Career Principal Investigator Award Final Report)

This project is researching FAST, a methodology to build very fast, cycle-accurate full system computer simulators and building the first set of such simulators and the first set of tools to help construct those simulators. The methodology relies on a functional model that is a fast, full-system but not cycle-accurate simulator coupled with a timing model that is models the micro-architectural structure and arbitration of a computer system, but not its functionality. The way FAST simulators differ from other simulators partitioned in the same way is that the interface between the functional and timing model is optimized to minimize the need for round-trip communication. The optimized communication enables FAST timing models to be implemented in an FPGA and the functional model in software while still achieving extremely high performance. Our general strategy is to design a methodology and then prototype an example using that methodology to ensure the methodology is sound before committing to it. This strategy ensures that the selected methodology has been tested and provides an early example of the output of that methodology.

97 MATHEMATICS AND COMPUTING↗

Computing Properties of Hadrons, Nuclei and Nuclear Matter from Quantum Chromodynamics

This project was part of a coordinated software development effort which the nuclear physics lattice QCD community pursues in order to ensure that lattice calculations can make optimal use of present, and forthcoming leadership-class and dedicated hardware, including those of the national laboratories, and prepares for the exploitation of future computational resources in the exascale era. The UW team improved and extended software libraries used in lattice QCD calculations related to multi-nucleon systems, enhanced production running codes related to load balancing multi-nucleon production on large-scale computing platforms, and developed SQLite (addressable database) interfaces to efficiently archive and analyze multi-nucleon data and developed a Mathematica interface for the SQLite databases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

ADVANCED SIMULATION CAPABILITY FOR ENVIRONMENTAL MANAGEMENT- CURRENT STATUS AND PHASE II DEMONSTRATION RESULTS

The U.S. Department of Energy (USDOE) Office of Environmental Management (EM), Office of Soil and Groundwater, is supporting development of the Advanced Simulation Capability for Environmental Management (ASCEM). ASCEM is a state-of-the-art scientific tool and approach for understanding and predicting contaminant fate and transport in natural and engineered systems. The modular and open source high-performance computing tool facilitates integrated approaches to modeling and site characterization that enable robust and standardized assessments of performance and risk for EM cleanup and closure activities. The ASCEM project continues to make significant progress in development of computer software capabilities with an emphasis on integration of capabilities in FY12. Capability development is occurring for both the Platform and Integrated Toolsets and High-Performance Computing (HPC) Multiprocess Simulator. The Platform capabilities provide the user interface and tools for end-to-end model development, starting with definition of the conceptual model, management of data for model input, model calibration and uncertainty analysis, and processing of model output, including visualization. The HPC capabilities target increased functionality of process model representations, toolsets for interaction with Platform, and verification and model confidence testing. The Platform and HPC capabilities are being tested and evaluated for EM applications in a set of demonstrations as part of Site Applications Thrust Area activities. The Phase I demonstration focusing on individual capabilities of the initial toolsets was completed in 2010. The Phase II demonstration completed in 2012 focused on showcasing integrated ASCEM capabilities. For Phase II, the Hanford Site deep vadose zone (BC Cribs) served as an application site for an end-to-end demonstration of capabilities, with emphasis on integration and linkages between the Platform and HPC components. Other demonstrations, addressing attenuation-based remedies at the Savannah River Site F Area and performance assessment for a representative waste tank, illustrate integration of linked ASCEM capabilities and initial integration efforts with tools from the Cementitious Barriers Partnership.

54 ENVIRONMENTAL SCIENCES↗

ADVANCED SIMULATION CAPABILITY FOR ENVIRONMENTAL MANAGEMENT – CURRENT STATUS AND PHASE II DEMONSTRATION RESULTS

The U.S. Department of Energy (USDOE) Office of Environmental Management (EM), Office of Soil and Groundwater, is supporting development of the Advanced Simulation Capability for Environmental Management (ASCEM). ASCEM is a state-of-the-art scientific tool and approach for understanding and predicting contaminant fate and transport in natural and engineered systems. The modular and open source high-performance computing tool facilitates integrated approaches to modeling and site characterization that enable robust and standardized assessments of performance and risk for EM cleanup and closure activities. The ASCEM project continues to make significant progress in development of computer software capabilities with an emphasis on integration of capabilities in FY12. Capability development is occurring for both the Platform and Integrated Toolsets and High-Performance Computing (HPC) Multiprocess Simulator. The Platform capabilities provide the user interface and tools for end-to-end model development, starting with definition of the conceptual model, management of data for model input, model calibration and uncertainty analysis, and processing of model output, including visualization. The HPC capabilities target increased functionality of process model representations, toolsets for interaction with Platform, and verification and model confidence testing. The Platform and HPC capabilities are being tested and evaluated for EM applications in a set of demonstrations as part of Site Applications Thrust Area activities. The Phase I demonstration focusing on individual capabilities of the initial toolsets was completed in 2010. The Phase II demonstration completed in 2012 focused on showcasing integrated ASCEM capabilities. For Phase II, the Hanford Site deep vadose zone (BC Cribs) served as an application site for an end-to-end demonstration of capabilities, with emphasis on integration and linkages between the Platform and HPC components. Other demonstrations, addressing attenuation-based remedies at the Savannah River Site F Area and performance assessment for a representative waste tank, illustrate integration of linked ASCEM capabilities and initial integration efforts with tools from the Cementitious Barriers Partnership.

DOE Environmental Management, advanced simulation,↗

Portals Reference Implementation v. 1.0

The Portals reference implementation is based on the Portals 4.X API, published by Sandia National Laboratories as a freely available public document. It is designed to be an implementation of the Portals Networking Application Programming Interface and is used by several other upper layer protocols like SHMEM, GASNet and MPI. It is implemented over existing networks, specifically Ethernet and InfiniBand networks. This implementation provides Portals networks functionality and serves as a software emulation of Portals compliant networking hardware. It can be used to develop software using the Portals API prior to the debut of Portals networking hardware, such as Bull’s BXI interconnect, as well as a substitute for portals hardware on development platforms that do not have Portals compliant hardware. The reference implementation provides new capabilities beyond that of a typical network, namely the ability to have messages matched in hardware in a way compatible with upper layer software such as MPI or SHMEM. It also offers methods of offloading network operations via triggered operations, which can be used to create offloaded collective operations. Specific details on the Portals API can be found at http://portals4.org.

Grant, Ryan E.↗

Overview of System Integration Analysis Activities for Integrated Waste Management

Spent nuclear fuel (SNF) generated by the current fleet of commercial nuclear reactors is being stored at the reactor sites in spent fuel pools (SFPs) and in dry independent spent fuel storage installations (ISFSIs). The US Department of Energy Office of Nuclear Energy (DOE-NE) is developing an Integrated Waste Management Program (IWMP) comprising a suite of options and supporting analyses to enable future informed choices. The IWMP is organized into the following five major areas: 1) Consent-Based Siting, 2) IWM Facilities and Equipment Concepts and Development, 3) Transportation Capability Analysis and Support, 4) Information Technology Solutions and Support, and 5) System Integration Analysis and Support. This paper discusses the activities ongoing in the IWMP System Integration Analysis and Support area. Two main areas of research in system integration are data and tools development, as well as system analysis assessments. One of the tools being developed in the system integration area is the Used Nuclear Fuel-Storage, Transportation & Disposal Analysis Resource and Data System (UNF-ST&DARDS) tool. It is being developed as a foundational resource for DOE-NE to manage SNF data, along with several compatible analysis tools for time-dependent characterization of SNF and related systems. UNF-ST&DARDS has the unparalleled ability to track SNF through the entire back end of the fuel cycle—from the time the fuel is discharged from a reactor through its disposal in a geological repository. UNF ST&DARDS interfaces with the SCALE code system for nuclear analysis and COBRA-SFS for thermal analysis. Another main tool being developed is the Next Generation System Analysis Model (NGSAM). NGSAM is an agent-based simulation software tool expressly designed to be capable of modeling the waste management system. NGSAM has been developed to enable informed decision-making by providing the capability of analyzing various potential system options for the management of SNF and HLW. Using NGSAM, system architecture analyses are being conducted to support the future deployment of a comprehensive nuclear waste management system that considers all major back-end aspects of the nuclear fuel cycle (i.e., transportation, storage, and disposal). System analysis assessments may investigate the implications of various strategies such as different acceptance rates, acceptance queues, facility capacities and options, standardized canisters, and different assumed system operation start dates. Recently, some system analysis effort has begun to look at how the waste management system might operate for advanced reactor fuel cycles.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Opdefender Network Monitoring And Control System

OpDefender is a new system designed to enhance the cyber security of control system networks. It accomplishes this by inspecting each network packet using a novel, patent-pending method that extends software defined networking into the application/ICS protocol layer. OpDefender consists of two key components: 1. Smart, “ICS-aware” network switches that analyze and filter network traffic in real time. 2. A network management human machine interface (HMI) that allows an operator to monitor and control network traffic in real time. The “ICS-aware” switches can serve as a drop-in replacement for typical network switches, or they can be used in conjunction with existing network switches. OpDefender is configured and controlled in real time via a custom-built, web-based HMI designed with the operator in mind.

Johnson, BriamE.↗

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗

Supply Chain-Based Solution to Prevent Fuel Tax Evasion: Final Report

The primary source of funding for the United States transportation system is derived from motor fuel and other highway use taxes. Loss of revenue attributed to fuel-tax evasion has been assessed to be somewhere between 1 billion and 3 billion per year. Any solution that addresses this problem needs to include not only the tax-collection agencies and auditors, but also the carriers transporting oil products and the carriers customers. This report presents a system developed by the Oak Ridge National Laboratory (ORNL) for the Federal Highway Administration which has the potential to reduce or eliminate many fuel-tax evasion schemes. The solution balances the needs of tax-auditors and those of the fuel-hauling companies and their customers. The system has three main components. The on-board subsystem combined sensors, tracking and communication devices, and software (the on-board Evidential Reasoning System, or obERS) to detect, monitor, and geo-locate the transfer of fuel among different locations. The back office sub-system (boERS) used self-learning algorithms to determine the legitimacy of the fuel loading and offloading (important for tax auditors) and detect potential illicit operations such as fuel theft (important for carriers and their customers, and may justify the deployment costs). The third sub-system, the Fuel Distribution and Auditing System or FDAS, is a centralized database, which together with a user interface allows tax auditors to query the data submitted by the fuel-hauling companies and correlate different parameters to quickly identify any anomalies. Industry partners included Barger Transport of Weber City, Virginia (fleet); Air-Weigh, of Eugene, Oregon (and their wires and harnesses); Liquid Bulk Tank (LBT) of Omaha, Nebraska (three five-compartment trailers); and Innovative Software Engineering (ISE) of Coralville, Iowa(on-board telematics device and back-office system). ORNL conducted a pilot test with the three instrumented vehicles collecting real-world data during an eight-month period (October 2014 to June 2015). The vehicles logged a total of 375,000 miles and transported more than 7.5 million gallons of fuel. The drivers entered information on the telematics device about 77% of the time, with about 15% (10%) of the data showing at least one compartment with loading (offloading) valve activity, but not driver information entry for that compartment. Seven events (or about 0.7% of the trips) were identified by the boERS as having a missing fuel diversion number. The solution developed and tested in the pilot test had federal- and state-level tax auditors as its main audience. Nonetheless, the technology has to be adopted by the fuel carriers and therefore the solution had to address the needs of fuel-hauling companies and their customers (i.e., fuel theft and cocktailing). Sensors in the hatches allowed the obERS recognize when one of those were opened (always a suspicious activity, unless it happens at locations where maintenance is performed on the vehicle). The fuel-theft issue was addressed by a self-learning algorithm deployed on the boERS that continuously processed the data from the field to construct probability distributions of measures such as elapsed time of fuel loading and offloading by driver, vehicle, and compartment, valve actuation sequence, elapsed time between the first two valve actuations (by driver, compartment, and location), and other parameters. Probability thresholds, which can be set up by the carrier, determined how to classify the observed events. The boERS also kept track of valve sequencing at a given location and analyzed these actuations to help identify any suspicious activities. Technical and economic recommendations include: a) simplification of the driver data-entry task; b) reduction of system deployment cost; c) addition of capabilities that make the system more appealing to industry (i.e., identify and avoid fuel misdelivery); and d) incorporation of additional capabilities to the FDAS. Path to commercialization recommendations include: a) identify a company willing to further develop, test, and certify a hardened system with a price point the market will bear; b).transfer ERS to licensee; c) establish a fleet or fleets who want this technology for carrier benefits or trailer manufacturer who wants to offer it as optional technology; and d) identify a location for the deployment of FDAS.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Web servers and services for electrostatics calculations with APBS and PDB2PQR

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.

99 GENERAL AND MISCELLANEOUS↗