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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Cabana: A Performance Portable Library for Particle-Based Simulations

Particle-based simulations are ubiquitous throughout many fields of computational science and engineering, spanning the atomistic level with molecular dynamics (MD), to mesoscale particle-in-cell (PIC) simulations for solid mechanics, device-scale modeling with PIC methods for plasma physics, and massive N-body cosmology simulations of galaxy structures, with many other methods in between (Hockney & Eastwood, 1989). While these methods use particles to represent significantly different entities with completely different physical models, many low-level details are shared including performant algorithms for short- and/or long-range particle interactions, multi-node particle communication patterns, and other data management tasks such as particle sorting and neighbor list construction. Cabana is a performance portable library for particle-based simulations, developed as part of the Co-Design Center for Particle Applications (CoPA) within the Exascale Computing Project (ECP) (Alexander et al., 2020). The CoPA project and its full development scope, including ECP partner applications, algorithm development, and similar software libraries for quantum MD, is described in (Mniszewski et al., 2021). Cabana uses the Kokkos library for on-node parallelism (Edwards et al., 2014; Trott et al., 2022), enabling simulation on multi-core CPU and GPU architectures, and MPI for GPU-aware, multi-node communication. Cabana provides particle simulation capabilities on almost all current Kokkos backends, including serial execution, OpenMP (including OpenMP-Target for GPUs), CUDA (NVIDIA GPUs), HIP (AMD GPUs), and SYCL (Intel GPUs), providing a clear path for the coming generation of accelerator-based exascale hardware. Cabana builds on Kokkos by providing new particle data structures and particle algorithms resulting in a similar execution policy-based, node-level programming model that is intended to be used in addition to the core Kokkos library within an application. Cabana is designed as an application and physics agnostic, but particle-specific toolkit which can either be used to generate a new application, or to be used as needed in existing applications at various levels of invasiveness including through interfaces that wrap user memory in existing data structures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Coupled Physics Environment (CouPE) library - Design, Implementation, and Release

Over several years, high fidelity, validated mono-physics solvers with proven scalability on peta-scale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a unified mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. In this report, we present details on the design decisions and developments on CouPE, an acronym that stands for Coupled Physics Environment that orchestrates a coupled physics solver through the interfaces exposed by MOAB array-based unstructured mesh, both of which are part of SIGMA (Scalable Interfaces for Geometry and Mesh-Based Applications) toolkit. The SIGMA toolkit contains libraries that enable scalable geometry and unstructured mesh creation and handling in a memory and computationally efficient implementation. The CouPE version being prepared for a full open-source release along with updated documentation will contain several useful examples that will enable users to start developing their applications natively using the native MOAB mesh and couple their models to existing physics applications to analyze and solve real world problems of interest. An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is also being investigated as part of the NEAMS RPL, to tightly couple neutron transport, thermal-hydraulics and structural mechanics physics under the SHARP framework. This report summarizes the efforts that have been invested in CouPE to bring together several existing physics applications namely PROTEUS (neutron transport code), Nek5000 (computational fluid-dynamics code) and Diablo (structural mechanics code). The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The design of CouPE along with motivations that led to implementation choices are also discussed. The first release of the library will be different from the current version of the code that integrates the components in SHARP and explanation on the need for forking the source base will also be provided. Enhancements in the functionality and improved user guides will be available as part of the release. CouPE v0.1 is scheduled for an open-source release in December 2014 along with SIGMA v1.1 components that provide support for language-agnostic mesh loading, traversal and query interfaces along with scalable solution transfer of fields between different physics codes. The coupling methodology and software interfaces of the library are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the CouPE library.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

Annex C. Data Libraries for IAEA Nuclear Security Assessment Methodologies (NUSAM)

Data Libraries are a collection of experimental data for PP elements based on specific defeat mechanisms. The data can de related to probability of detection, assessment, or barrier delay times. The data libraries can be a manually tabulated list or an electronic menu values enbedded in a stand-alone database or in an assessment software program such as SAVI or EASI. Data library values are usually based on years of historical testing data for many forms of common and sometimes unique PPS systems. Most useful testing libraries include data from the most basic alarm sensors, doors, walls, and barriers to very sophisticated PP elements. Each PP element is tested using increasing levels of defeat techniques from hand tools, power tools, breaching tools, explosives, and vehicles, as applicable.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2018

Verification of the MC2-3 Gamma Library

The new gamma library was generated based on the 94-group gamma structure, including delayed gamma and beta data, using the PreGAMMA and GenGAMMA codes with ENDF/BVII. 0 data. The new gamma library was first verified using the 2D benchmark problems that were introduced in the GAMSOR manual, showing that the neutron and gamma heatings from DIF3D were in good agreement with MCNP solutions within 5% even in the non-fuel regions of both cores with uranium or plutonium dominant fuel compositions. Similarly, the DIF3D power solutions for additional simpler 1D problems with 3 or 6 regions showed good agreement with MCNP solutions. Note that all DIF3D calculations were based on the 230- group neutron and 94-group gamma data. For the EBR-II benchmark problem, the DIF3D solution with the new gamma library maintained good agreement in the power distribution with the MCNP solution, which is comparable to the DIF3D results with the current 21-group gamma library. The use of delayed gamma and beta data increased powers at the dummy assemblies by 26%, which appears to be reasonable. Further detailed verification tests may be necessary and, more importantly, validation tests are required against measurement data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Towards Use of Mixed Precision in ECP Math Libraries [Exascale Computing Project]

The use of multiple types of precision in mathematical software has the potential to increase its performance on new heterogeneous architectures. The xSDK project focuses both on the investigation and development of multiprecision algorithms as well as their inclusion into xSDK member libraries. This report summarizes current efforts on including and/or using mixed precision capabilities in the math libraries Ginkgo, heFFTe, hypre, MAGMA, PETSc/TAO, SLATE, SuperLU, and Trilinos, including KokkosKernels. It contains both numerical results from libraries that already provide mixed precision capabilities, as well as descriptions of the strategies to incorporate multiprecision into established libraries.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Towards Use of Mixed Precision in ECP Math Libraries

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Standardizing a Renewed Fission Product Yield Library and Related Covariances (Part II)

A complete library of independent fission product yields including covariance information was generated by a sequential Bayesian methodology whose prior information consisted of independent fission product yields and branching ratios of the possible decay modes reported in the recently released ENDF/B-VIII.0 nuclear data library. The Bayesian procedure consisted in the adjustment of independent fission product yields to match the set of stable and long-lived cumulative yields reported in the ENDF/B-VIII.0 nuclear data library which, in this work, were considered as legacy values together with their uncertainties. According to the χ 2 -metric, the results obtained by this methodology show a systematic improvement in the agreement with legacy reported cumulative yields for the entire adjusted independent fission product yield library.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Transient Efficiency Flexibility and Reliability Optimization of Coal-Fired Power Plants (Model-Based Estimation Library Report)

This document pertains to the reporting requirements of DOE contract FE-0031767. The document covers the development of a model-based estimation (MBE) library for generating digital twins of coal-fired power plants (CFPPs). The models used by the MBE are transient and physics-based. Model classes in the library that correspond to different components in CFPPs are presented with physical explanations and representative results. MBE library provides Extended Kalman Filter (EKF), and Unscented Kalman Filter (UKF) algorithms. The MBE library is generic and can be used to represent a variety of CFPPs. A digital twin of a CFPP will be created as the reduced-order model of that CFPP is embedded in the developed MBE architecture.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2024

Evaluated Nuclear Data Library, with ENDL2009.5-direct (2009.5 Rev.)

LLNL’s Nuclear Data and Theory Group have created a 2009.5 revised release of the Evaluated Nuclear Data Library (ENDL2009.5). This library is designed to support LLNL’s current and future nuclear data needs and will be employed in nuclear reactor, nuclear security and stockpile stewardship simulations with ASC codes. The ENDL2009 database was the most complete nuclear database for Monte Carlo and deterministic transport of neutrons and charged particles. It was assembled with strong support from the ASC PEM and Attribution programs, leveraged with support from Campaign 4 and the DOE/Office of Science’s US Nuclear Data Program. This document lists the revisions and fixes made in a new release called ENDL2009.5, by comparing with the existing data in the previous releases ENDL2009.3 and ENDL2009.4. In addition to the legacy library ENDL2009.5 from ENDL-format files generated by Fete, an ENDL2009.5-direct library is also released, in which ENDF6-formatted sources are used wherever possible to avoid possible translation errors from Fete.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Terra-Populus v0.1: A Python Library for LandScan High-Definition Population Analysis and Modeling

The terra-populus library is designed for use by the LandScan HD technical team, offering a streamlined set of tools for generating and updating LandScan HD datasets from foundational building-level data, referred to as 'molecules,' provided by the building-level attribution team. This document serves as the primary technical documentation for terra-populus. Version 0.1 of the library includes the core modeling components necessary for LandScan HD production. It enables the generation of the LandScan HD Baseline dataset as well as corresponding confidence measures for the occupancy rates used. Parameters have been included for incorporating damaged building indicators and changes in population, to faciliate the creation of rapid updates for LandScan HD. Future iterations of terra-populus will introduce tools for creating a confidence index, and quantifying and propagating uncertainty, facilitating the creation of probabilistic LandScan HD outputs. This report provides an overview of the tools available in the library and the corresponding code implementations. One of the key advancements implemented in terra-populus is a redefinition of the atomic modeling unit for LandScan HD. Traditionally, the LandScan HD vector analytical framework has generated population estimates at the building sub-component (molecule) level. However, terra-populus adopts a building-level modeling approach. This shift is an operational decision aimed at aligning LandScan HD outputs with confidence measures, which are computed and validated at the building level (confidence measures are not included in this version of terra-populus, aside from those associated with the occupancy rates). Additional advancements to the LandScan HD modeling, as implemented by terra-populus, include a minimum population value parameter and an auto assignment of building floor counts. The population minimum value was implemented to prevent buildings and subsequent LandScan HD pixels that contained small values that may not rasterize in production. An 'auto' value has been included as a method for dealing with buildings lacking floor count information, where it is the average floor count of all other buildings with a residential building use type tag. The logic behind this is to remain consistent with the current logic employed for dealing with building use type null instances, where a null use type is defaulted to residential since it is the most common building type. The auto logic is intended to apply the most common building floor count of the most common type of buildings. The tools provided in terra-populus represent a significant step forward in improving the efficiency, reproducibility, and transparency of the LandScan HD modeling process. As the library evolves, it will continue to serve as a foundational resource for high-resolution population modeling.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2026

Public Release of the MENDF80 and MT80 Nuclear Data Libraries for NDI

This document describes the MENDF80 and MT80 data libraries, which are multi-group neutron cross section libraries based on ENDF/B-VIII.0 for LANL’s Nuclear Data Interface (NDI). MENDF80 is a downscatter-only library, while MT80 is multi-temperature. Both libraries also have 30-group pre-collapsed versions, MENDF80 30 and MT80 30.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples

Comprehensive and unambiguous identification of small molecules in complex samples will revolutionize our understanding of the role of metabolites in biological systems. Existing and emerging technologies have enabled measurement of chemical properties of molecules in complex mixtures and, in concert, are sensitive enough to resolve even stereoisomers. Despite these experimental advances, small molecule identification is inhibited by (i) chemical reference libraries (e.g. mass spectra, collision cross section, and other measurable property libraries) representing <1% of known molecules, limiting the number of possible identifications, and (ii) the lack of a method to generate candidate matches directly from experimental features (i.e. without a library). To this end, we developed a variational autoencoder (VAE) to learn a continuous numerical, or latent, representation of molecular structure to expand reference libraries for small molecule identification. We extended the VAE to include a chemical property decoder, trained as a multitask network, in order to shape the latent representation such that it assembles according to desired chemical properties. The approach is unique in its application to metabolomics and small molecule identification, with its focus on properties that can be obtained from experimental measurements (m/z, CCS) paired with its training paradigm, which involved a cascade of transfer learning iterations. First, molecular representation is learned from a large dataset of structures with m/z labels. Next, in silico property values are used to continue training, as experimental property data is limited. Finally, the network is further refined by being trained with the experimental data. This allows the network to learn as much as possible at each stage, enabling success with progressively smaller datasets without overfitting. Once trained, the network can be used to predict chemical properties directly from structure, as well as generate candidate structures with desired chemical properties. Our approach is orders of magnitude faster than first-principles simulation for CCS property prediction. Additionally, the ability to generate novel molecules along manifolds, defined by chemical property analogues, positions DarkChem as highly useful in a number of application areas, including metabolomics and small molecule identification, drug discovery and design, chemical forensics, and beyond.

Colby, Sean M↗

DOE OSTI2013

Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries

Recent advances in sequencing technologies generate new predictions and hypotheses about the functional roles of environmental microorganisms. Yet, until we can test these predictions at a scale that matches our ability to generate them, most of them will remain as hypotheses. Function-based mining of metagenomic libraries can provide direct linkages between genes, metabolic traits and microbial taxa and thus bridge this gap between sequence data generation and functional predictions. Here we developed high-throughput screening assays for function-based characterization of activities involved in plant polymer decomposition from environmental metagenomic libraries. The multiplexed assays use fluorogenic and chromogenic substrates, combine automated liquid handling and use a genetically modified expression host to enable simultaneous screening of 12,160 clones for 14 activities in a total of 170,240 reactions. Using this platform we identified 374 (0.26%) cellulose, hemicellulose, chitin, starch, phosphate and protein hydrolyzing clones from fosmid libraries prepared from decomposing leaf litter. Sequencing on the Illumina MiSeq platform, followed by assembly and gene prediction of a subset of 95 fosmid clones, identified a broad range of bacterial phyla, including Actinobacteria, Bacteroidetes, multiple Proteobacteria sub-phyla in addition to some Fungi. Carbohydrate-active enzyme genes from 20 different glycoside hydrolase (GH) families were detected. Using tetranucleotide frequency (TNF) binning of fosmid sequences, multiple enzyme activities from distinct fosmids were linked, demonstrating how biochemically-confirmed functional traits in environmental metagenomes may be attributed to groups of specific organisms. Overall, our results demonstrate how functional screening of metagenomic libraries can be used to connect microbial functionality to community composition and, as a result, complement large-scale metagenomic sequencing efforts.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1985

The library system of the DFVLR: Present status, planned reorganization, user possibilities

This paper gives an overview of the present status, planned alterations, and the scope of users of the DFVLR library, as well as a survey of library related activities outside of the library department. Attention is given to the tasks of the DFVLR which include research, assistance in planning and carrying out projects, and the construction and operation of large test installations, showing how they relate to demands on the library.

Sternemann, P.↗

NASA NTRS1987

Raster graphics display library

The Raster Graphics Display Library (RGDL) is a high level subroutine package that give the advanced raster graphics display capabilities needed. The RGDL uses FORTRAN source code routines to build subroutines modular enough to use as stand-alone routines in a black box type of environment. Six examples are presented which will teach the use of RGDL in the fastest, most complete way possible. Routines within the display library that are used to produce raster graphics are presented in alphabetical order, each on a separate page. Each user-callable routine is described by function and calling parameters. All common blocks that are used in the display library are listed and the use of each variable within each common block is discussed. A reference on the include files that are necessary to compile the display library is contained. Each include file and its purpose are listed. The link map for MOVIE.BYU version 6, a general purpose computer graphics display system that uses RGDL software, is also contained.

Grimsrud, Anders↗

NASA NTRS1989

AdaNET prototype library administration manual

The functions of the AdaNET Prototype Library of Reusable Software Parts is described. Adopted from the Navy Research Laboratory's Reusability Guidebook (V.5.0), this is a working document, customized for use the the AdaNET Project. Within this document, the term part is used to denote the smallest unit controlled by a library and retrievable from it. A part may have several constituents, which may not be individually tracked. Presented are the types of parts which may be stored in the library and the relationships among those parts; a concept of trust indicators which provide measures of confidence that a user of a previously developed part may reasonably apply to a part for a new application; search and retrieval, configuration management, and communications among those who interact with the AdaNET Prototype Library; and the AdaNET Prototype, described from the perspective of its three major users: the part reuser and retriever, the part submitter, and the librarian and/or administrator.

Hanley, Lionel↗

NASA NTRS1991

Proposal for a CLIPS software library

This paper is a proposal to create a software library for the C Language Integrated Production System (CLIPS) expert system shell developed by NASA. Many innovative ideas for extending CLIPS were presented at the First CLIPS Users Conference, including useful user and database interfaces. CLIPS developers would benefit from a software library of reusable code. The CLIPS Users Group should establish a software library-- a course of action to make that happen is proposed. Open discussion to revise this library concept is essential, since only a group effort is likely to succeed. A response form intended to solicit opinions and support from the CLIPS community is included.

Porter, Ken↗

NASA NTRS1993

Intel NX to PVM 3.2 message passing conversion library

NASA Langley Research Center has developed a library that allows Intel NX message passing codes to be executed under the more popular and widely supported Parallel Virtual Machine (PVM) message passing library. PVM was developed at Oak Ridge National Labs and has become the defacto standard for message passing. This library will allow the many programs that were developed on the Intel iPSC/860 or Intel Paragon in a Single Program Multiple Data (SPMD) design to be ported to the numerous architectures that PVM (version 3.2) supports. Also, the library adds global operations capability to PVM. A familiarity with Intel NX and PVM message passing is assumed.

Arthur, Trey↗