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The Geophysical Monitoring Program Core Seismic Libraries contain a broad array of seismic and waveform analysis libraries useful for a wide range of seismic analysis processes. These include signal processing, travel time calculation, waveform correlation, array processing, geometry and geodesy, and plotting libraries.
Abstract Background Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library. Results We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index’s suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3’s FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is $$\sim $$ ∼ 2–4x faster than SeqAn3 for nucleotide search, and $$\sim $$ ∼ 2–6x faster for amino acid search; it is also $$\sim $$ ∼ 4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage. Conclusions AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.
Five multigroup libraries are discussed for external release. They are e68g_103, a multigroup photon library, and mendf80, mt80, mendf80_30 and mt80_30 are multigroup neutron libraries.
The C-NR Countroom analyzes gamma spectroscopy data using three codes, SAP (which is the combination of SPECANAL and RAYGUN), GAMANAL and UNISAMPO. The codes use libraries which are chosen by the user of gamma emission data to do the identification and quantification. The Countroom maintains nine unique libraries for use in analysis. Historically, the values contained in these libraries has not been consistently updated and many values are quite old and do not reflect the state-of-the-art.
This document is the final report on the status and developments of the Charged-Particle Transport (CPT) Level-2 (“CP2020”) ASC/PEM Milestone work. This section gives an overview of the CP2020 work partitioned into two subsections: 1) a summary of the code tools used for generating CP (and other) data in Section 1.2; and 2) and library data and codes access information for end users in Section 1.3. Section 2 gives an overview of the status of previous work on charged-particle (CP) nuclear data, particularly focused on the work of the FY2011 CP Level-2 Milestone. New work for CP2020 is detailed in the following Section 3. Section 4 discusses testing and validation of the evaluated and processed data for the CP2020 library. Conclusions based on the experience of this Level-2 work and the outlook for future development of CPT-relevant data are given in the final Section 5. Appendices, detailed throughout the report, are provided for further information. This report, related documentation, codes, and the CPT nuclear data libraries are available via online repository.
Today is the National Security Research Center’s second anniversary. These two years, though, have been eight decades in the making, said NSRC Director Riz Ali. “We opened our doors in 2019, but the Center’s beginnings date back to World War II when J. Robert Oppenheimer created the Lab in Los Alamos to develop the first-ever nuclear weapons,” Ali said. “An important part of opening the Lab included standing up a technical reports library. Since then, we have amassed millions of holdings and today we are one of the top research institutions in the country.” What had long-been a repository of classified archival materials is today a dynamic, vibrant library that outsizes the collections of other similar research libraries around the country. Today, the NSRC houses the Laboratory’s classified nuclear weapons research, data and reports, as well as unclassified historical artifacts – the stories, photos, films and more from the people who have been a part of the Lab from the start.
As our Lab was being created nearly 80 years, J. Robert Oppenheimer handpicked Charlotte Serber for what he considered one of the most critical positions: to oversee the wartime technical library. Today, serving as the director of the National Security Research Center (NSRC), I can attest to both the importance of Oppie’s pick and affirm that he made the right choice. The NSRC is the Lab’s classified library and we’ve evolved from that inaugural wartime technical library. Thanks to Serber, those materials remain a vital part of our collections today.
Just think of these sample relics: A step-by-step manual on how to assemble a Fat Man atomic bomb. A patent application for the world’s first nuclear weapons. Laboratory notebooks of Nobel laureates. And much more. The collections at the National Security Research Center (NSRC) contain millions of historical materials and traces its origin to the Technical Library started by J. Robert Oppenheimer in 1943 as part of the Manhattan Project, which was the U.S. government’s top-secret effort to create the first atomic bombs. Since then, these collections have grown and are relied upon by today’s scientists, engineers, and researchers who support our national security mission. The NSRC is the Lab’s classified library that also houses unclassified legacy materials. In recognition of National Library Week (April 3 - 9), staff from the NSRC picked some of their favorite pieces of preserved Laboratory history.
This report provides the documentation for the revised procedure to generate the MC 2 -3 gamma library with the latest versions of PreGAMMA and GenGAMMA which have recently been updated to fix the program errors and inconsistent data processing for some isotopes identified in a recent verification and validation study of the MC 2 -3 gamma library. A few associated errors associated with gamma processing were also identified and fixed in the MC 2 -3 code. Addressing the changes in MC 2 -3, the procedure to generate the PMATRX and GAMISO datasets is discussed as well. The input data of PreGAMMA and GenGAMMA are discussed in detail using sample input data. In addition, the structure and formats of the MC 2 -3 gamma library are provided in detail.
This report describes the second edition of the Pseudocap Strength models for porous rocks implemented in GEODYN material library. The first model was developed in 2007 and calibrated for concrete. Then, the model parameters were calibrated based on triaxial tests reported for limestones and sandstones of various porosities. In these models some key parameters were chosen as functions of the reference porosity,Φ. Since then multiple modifications were implemented in the model, therefore, it has been recalibrated for some common porous materials such as limestones, sandstones, alluvium, tuffs and granite. Two types of models are described in this repot. The first type (called Pseudocap Model or PM) is for rocks from a specific location. Parameters were calibrated for several specific geologic materials. The second type (called Generic Pseudocap Model or GPM) is useful for the sites where only basic information (rock type, porosity) is available. Generic models include built-in correlations between porosities and other mechanical properties observed for certain rock types. The models of both types were validated by comparing not only to quasi-static triaxial tests for these materials but also to shock Hugoniot data and spherical explosion data for some materials. All models were derived in the frame of isotropic plasticity. They are designed to be used in explicit finite element/difference codes. Tangent stiffness tensor is not provided but can be calculated numerically for the model to be used in implicit finite element codes. For an isotropic material the stress can be decomposed into volumetric and deviatoric parts. The volumetric part is modeled using an Equation of state (EOS) which calculates the pressure and the bulk sound speed as functions of the internal specific energy and density. Here a simple, Mie-Gruneisen EOS is presented, but tabulated EOS (LEOS) provided by the library can be used as well. The stress is limited by the yield surface which depends on three invariants of the stress tensor and specific internal energy. In addition, to capture the strain-rate dependence a simple multiplier is used for the yield surface which depends on the equivalent plastic strain rate. The failure surface (the ultimate yield, Y f , defined later) is chosen in the Hoek-Brown form, commonly used in rock mechanics. It includes measurable parameters such as Unconfined Compressive Strength (UCS) as well as scale parameters characterizing the quality of the rock such as GSI (Geologic Strength Index). Thus, even though the model is calibrated for small samples it offers a way to extrapolate the strength to the field scale using geological characterization of the rock mass. The model captures effects of brittle-ductile transition in rocks by introducing a cap multiplier to the yield function. The rate of dilatancy (bulking) is proportional to the slope of the yield surface affected by the cap. Therefore, it takes place only at low confinements when the pressure is less than the brittle-ductile transition pressure, P BD . On the contrary, the porous compaction takes place at pressures higher than P BD . The cap moves as the porosity is compacted or new porosity is generated due to dilatancy. The porous compaction is modeled using an evolution equation which includes deviatoric stress so that the onset of compaction corresponds to the cap surface. The model captures effects of shear-enhanced compaction which is an important for porous rocks. Section 2 describes the modeling framework and Section 3 presents the model calibration procedure. Section 4 compares experimental data for various rocks versus model predictions. The model parameters used for this comparison are given in Appendix. The files with material constants are available with the latest GEODYN material library distribution.
The C++ Standard Library is a valuable collection of generic algorithms and data structures that improves the usability and reliability of C++ software. Graph algorithms and data structures are notably absent from the standard library, and previous attempts to fill this gap have not gained widespread adoption. With the new addition of ranges and concepts in C++20, the language has the mechanisms to cleanly support generic graph algorithms as operations on a range of ranges. This report presents NWGraph, a generic C++ graph library for expressing graph algorithms in a modern, composable, and extensible, aka generic, fashion.
The Bioenergy Feedstock Library (BFL), part of the Biomass Feedstock National User Facility (BFNUF) located at INL, is a physical sample repository and a web-accessible electronic database. The BFL stores physical and chemical characteristics of biomass and waste carbon sources for energy use as well as samples generated from across U.S. Department of Energy (DOE) Bioenergy Technologies Office (BETO) and U.S. Department of Agriculture funded projects. The objective of this Bioenergy Feedstock Library Annual Summary Report for 2023 is to focus on the updates to (1) publicly available analytical data and equipment tracked through the BFNUF, (2) physical samples available for request, (3) sample and data archival progress from recent BETO-funded projects, and (4) publicly available datasets created upon request from BETO, INL projects, or outside entities compared to the 2022 Bioenergy Feedstock Library Annual Summary Report. This report highlights key statistics and available data and information important for INL, BFL users, academics, and industry.
This report provides an overview and update of the ongoing efforts to create a comprehensive library of microstructures for nuclear graphite and carbon-based materials under consideration for nuclear applications. The library includes data on microstructural characterization of unirradiated graphite materials, a guide to the techniques used to analyze graphite (which complements the ASME guidelines and ASTM standards), a summary of characterization data for neutron-irradiated or oxidized material, and a compendium of microstructural information for carbon-based materials. These efforts are being conducted at various length scales for the filler and binder phases in graphite to better understand graphite’s local structure and property relationships. This report is a follow-up to the previous milestone report titled Report on initial development of a database of nuclear graphite characteristics based on microstructural characterization, ORNL/TM/-2023/2992, published in July 2023.The effort to develop the library of microstructures supports the US Department of Energy Office of Advanced Reactor Technologies program objectives of aiding the material selection, licensing, management, and core assessments of a graphite core by documenting the unirradiated microstructure of relevant grades or characterizing the microstructure’s evolution under the reactor environment. Additionally, this project aims to provide (1) information and guidelines for the characterizing of graphite and (2) a protocol to assess a nuclear graphite grade.
MOOSE is a general purpose open source multiphysics framework supporting native finite element and finite volume discretizations as well and wrapping other libraries providing arbitrary computational capabilities. Due to its generality, it has experienced significant success. However, with recent changes in the landscape of computer architectures, most notably the growth of GPU computing, MOOSE must assess new technologies or else risk alienating customers interested in the benefits these technologies can offer. In that vein we have assessed multiple accelerator libraries developed through the ECP project, including Kokkos, libCEED, and MFEM, and present our evaluation of these libraries as candidates for incorporation into the MOOSE framework.
CMS has deployed a number of different GPU algorithms at the High-Level Trigger (HLT) in Run 3. As the code base for GPU algorithms continues to grow, the burden for developing and maintaining separate implementations for GPU and CPU becomes increasingly challenging. To mitigate this, CMS has adopted the Alpaka (Abstraction Library for Parallel Kernel Acceleration) library as the performance portability solution to provide a single-code base for parallel execution on both GPUs and CPUs in CMS software (CMSSW). A direct CUDA version of HCAL energy reconstruction, called Minimization At Hcal, Iteratively (MAHI), has been deployed at the HLT in the 2022-2023 data taking period. This contribution will describe how the CUDA version is converted into a portable implementation using the Alpaka library. We will discuss the porting experience from CUDA to Alpaka, the validation process and the performance of the Alpaka version in CPU and GPU.
This document describes a standard library plant controller model to interface with the grid-forming hybrid control inverter-based resource (IBR) model. The initial version of model specification was jointly developed by Pacific Northwest National Laboratory (PNNL), Tesla Energy, and EPRI, and it was revised multiple times later to incorporate suggestions from WECC MVS members. Tesla Energy provided main control algorithms to support the development of this model specification. This standard library model is developed to help the utility industry better understand the GFM technology. The model could be used to represent equipment for long-term planning studies where vendor-specific models are not available. As equipment matures and improves, standard library models will be updated to capture the new functionalities of GFMs. It is not intended that these models will always remain representative of all future GFM technologies.
Visolis is developing a commercial process for the bioproduction of a chemical intermediate, towards the derivative production of a portfolio of bio-based chemicals with large application potential, from drop-in commodity chemicals, to innovative specialty chemical offerings, to materials for multiple end markets and industries, which will ultimately benefit consumers and the public. Visolis already has several variants of a microbe that produce the chemical intermediate at distinct levels (i.e. high, medium, and low). They are currently pursuing transcriptomics analysis for some of these strains, towards a better understanding of the biology behind what makes certain strains perform better than others. There exist genome-scale library approaches for the microbe that could be used to screen gene disruption, overexpression, or repression candidates for perturbations to the production of the chemical intermediate. These approaches often reveal opportunities for further production improvement that are not otherwise accessible using hypothesis-driven metabolic engineering approaches. However, Visolis, while it could generate or procure such genome-scale libraries, does not have the automated strain engineering workflows required to screen thousands of variants, obtaining a production phenotype and a genotype for each. The purpose of this collaboration is to use LBNL and SNL capabilities to enable Visolis to effectively screen thousands of genome-scale library strain variants for phenotype/genotype relationships that will complement Visolis’ transcriptomic investigations.
This submission contains an open-source library of transient events in distributed system with high solar PV. The library includes the collected data, related documents and scripts for loading the data. The data library is built for transient event detection and machine learning based analysis algorithm development. The data was collected via both field test and software simulation. The units for the data are included in the data file headers for each data series. A text editor or spreadsheet software, such as Excel, and Matlab is required to view the data.