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DOE OSTI2023

Static versioning in the polyhedral model

An approach is presented to enhancing the optimization process in a polyhedral compiler by introducing compile-time versioning, i.e., the production of several versions of optimized code under varying assumptions on its run-time parameters. We illustrate this process by enabling versioning in the polyhedral processor placement pass. We propose an efficient code generation method and validate that versioning can be useful in a polyhedral compiler by performing benchmarking on a small set of deep learning layers defined for dynamically-sized tensors.

Meister, Benoit J.↗

DOE OSTI2024

Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication

When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The Global LAnd Surface Satellite (GLASS) evapotranspiration product Version 5.0: Algorithm development and preliminary validation

An accurate estimation of spatially and temporally continuous global terrestrial evapotranspiration (ET) is essential in the assessment of surface energy, water and carbon cycles. The Global LAnd Surface Satellite (GLASS) ET product Version 4.0 (v4.0) based on the Bayesian model averaging (BMA) method was generated to estimate global terrestrial ET. However, certain uncertainty for the GLASS ET product v4.0 limits its application. In this study, we introduced the deep neural networks (DNN) merging framework to improve terrestrial ET estimation for GLASS ET product Version 5.0 (v5.0) generation by integrating five satellite-derived ET products [Moderate Resolution Imaging Spectroradiometer (MODIS) ET product (MOD16), Shuttleworth–Wallace dual-source ET product (SW), Priestley–Taylor-based ET product (PT-JPL), modified satellite-based Priestley–Taylor ET product (MS-PT) and simple hybrid ET product (SIM)]. We compared the performance of DNN method against other merging methods, including GLASS ET algorithm v4.0 (BMA), the gradient boosting regression tree (GBRT) method and the random forest (RF) method, based on 195 global eddy covariance (EC) flux towers covering observations from 2000 through 2015. Validations indicated that the DNN had the highest accuracy among four merging methods across different land cover types, yielding the highest average determination coefficients (R 2 , 0.62), root-mean-squared-error (RMSE, 24.1 W/m 2 ) and Kling–Gupta efficiency (KGE, 0.77) with a of 99% confidence interval. Compared with GLASS ET algorithm v4.0, the DNN improved on the R 2 by approximately 7% (p < 0.01) and the KGE by 10%. Based on the DNN, we then generated 8-day GLASS ET product v5.0 globally with a 1 km spatial resolution from 2001 to 2015 driven by GLASS vegetation and surface net radiation (R n ) datasets and Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA2) datasets. Finally, this global terrestrial ET product provides a valuable dataset for monitoring regional and global water resources and environmental changes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

The Energy Exascale Earth System Model Version 3: 2. Overview of the Coupled System

The Energy Exascale Earth System Model version 3 (E3SMv3) represents the latest advancement in Earth system modeling developed by the U.S. Department of Energy (DOE). Building upon previous versions, E3SMv3 introduces significant updates across its coupled components to enhance capability and improve fidelity. The atmosphere component incorporates advancements in chemistry, aerosol-cloud interactions, convection, and microphysics. The ocean features a new time-stepping scheme and a higher-resolution unstructured mesh with sub-ice-shelf cavities, while the sea ice model integrates advanced snow and ice physics for more realistic cryospheric simulations. The land model introduces prognostic vegetation dynamics and a new sub-grid topographic treatment of solar radiation. A new tri-grid configuration harmonizes the horizontal grids of the land and river components for improved process coupling. It is enabled by a new non-linear remapping between the atmosphere and land. E3SMv3 underwent extensive testing through a comprehensive simulation campaign, including pre-industrial control, idealized CO 2 experiments, and historical simulations spanning 1850–2024. The model demonstrates significant improvements in simulating the evolution of the historical surface temperature, particularly addressing the “pothole cooling” bias in earlier versions. Reduced aerosol-related forcing contributes to more realistic radiative forcing and better alignment with the observational record. Ocean heat content (OHC) and sea ice trends are also improved as a result.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Emerging inorganic solar cell efficiency tables (version 2)

Abstract This paper presents the second version of the efficiency tables of materials considered as emerging inorganic absorbers for photovoltaic solar cell technologies. The materials collected in these tables are selected based on their progress in recent years, and their demonstrated potential as future photovoltaic absorbers. The first part of the paper consists of the guidelines for the inclusion of the different technologies in this paper, the verification means used by the authors, and recommendation for measurement best practices. The second part details the highest world-class certified solar cell efficiencies, and the highest non-certified cases (some independently confirmed). The third part highlights the new entries including the record efficiencies, as well as new materials included in this version of the tables. The final part is dedicated to review a specific aspect of materials research that the authors consider of high relevance for the scientific community. In this version of the efficiency tables, we are including an overview of the latest progress in quasi one-dimensional absorbers, such as antimony chalcogenides, for photovoltaic applications.

14 SOLAR ENERGY↗

DOE OSTI2022

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

Five versions of the Chlamydomonas reinhardtii reference genome have been produced over the last two decades. Here we present version 6, bringing significant advances in assembly quality and structural annotations. PacBio-based chromosome-level assemblies for two laboratory strains, CC-503 and CC-4532, provide resources for the plus and minus mating type alleles. We corrected major misassemblies in previous versions and validated our assemblies via linkage analyses. Contiguity increased over ten-fold and >80% of filled gaps are within genes. We used Iso-Seq and deep RNA-seq datasets to improve structural annotations, and updated gene symbols and textual annotation of functionally characterized genes via extensive manual curation. We discovered that the cell wall-less classical reference strain CC-503 exhibits genomic instability potentially caused by deletion of the helicase RECQ3, with major structural mutations identified that affect >100 genes. We therefore present the CC-4532 assembly as the primary reference, although this strain also carries unique structural mutations and is experiencing rapid proliferation of a Gypsy retrotransposon. We expect all laboratory strains to harbor gene-disrupting mutations, which should be considered when interpreting and comparing experimental results. Collectively, the resources presented here herald a new era of Chlamydomonas genomics and will provide the foundation for continued research in this important reference organism.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

HPXML Version Translator

HPXML is a consensus data transfer standard for residential buildings. Over several years, multiple versions of the standard have been released. This tool accepts an HPXML file in an older version and translates it to a newer version.

Merket, Noel↗

DOE OSTI2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Arctic shrub root traits, northern Alaska, summer 2017 (Version 2.0)

This data package contains root trait data collected from 170 plots of rapidly expanding shrub genera (Alnus, Betula, and Salix) and a widespread sedge (Eriophorum vaginatum) along a latitudinal and temperature gradient in northern Alaska. The trait data were collected in July 2017 and include root architecture (root diameter and branching patterns), mycorrhizal colonization (%), nitrogen concentration (%), delta 15N (per mil), and vertical root biomass. These raw data support a submitted manuscript that examines the distribution and interspecific variations of absorptive root traits of shrubs and graminoids across the graminoid-dominated nutrient-poor arctic tundra and reveals how deciduous shrub expansion affects plant nutrient acquisition strategies in tundra ecosystems. Data are presented by site (n=5) and patch (shrub or sedge plot) in separate csv files. The location data are provided in the “plot coordinates” file; all other files contain the data in the file title. Detailed methods are in Chen et al. (2020).2023/07/20 Update: The latest version of this dataset publication is version 2.0. The latest version of the data package was updated to include the alder nodule biomass dataset (alder nodule biomass.csv) and associated metadata (metadata_alder nodule biomass.csv). The name of the previous metadata file was updated (metadata_ root traits and biomass.csv ) to distinguish it from the new metadata file.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Data from: "A guide to using GitHub for developing and versioning data standards and reporting formats"

These data are the results of a systematic review that investigated how data standards and reporting formats are documented on the version control platform GitHub. Our systematic review identified 32 data standards in earth science, environmental science, and ecology that use GitHub for version control of data standard documents. In our analysis, we characterized the documents and content within each of the 32 GitHub repositories to identify common practices for groups that version control their documents on GitHub.In this data package, there are 8 CSV files that contain data that we characterized from each repository, according to the location within the repository. For example, in 'readme_pages.csv' we characterize the content that appears across the 32 GitHub repositories included in our systematic review. Each of the 8 CSV files has an associated data dictionary file (names appended with '_dd.csv' and here we describe each content category within CSV files.There is one file-level metadata file (flmd.csv) that provides a description of each file within the data package.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Arctic shrub size and leaf traits, northern Alaska, summer 2017 (Version 2.0)

This data package contains leaf and size trait and environmental data collected from 170 plots of rapidly expanding shrub genera (Alnus, Betula, and Salix) and a widespread sedge (Eriophorum vaginatum) along a latitudinal and climate gradient in northern Alaska. The trait data were collected in summer 2017 and include leaf area, specific leaf area, leaf nitrogen concentration, leaf delta 15N, leaf delta 13C, shrub height, aboveground biomass, and the ratio of root biomass to aboveground biomass. These raw data support a submitted manuscript that examines the intraspecific variations of size, leaf and root traits of shrubs across the graminoid-dominated nutrient-poor arctic tundra and reveals the environmental drivers of deciduous shrub traits in tundra ecosystems (Fraterrigo et al., submitted). Data are presented by site (n=5) and patch (shrub or sedge plot) in separate csv files. The location data are provided in the “plot coordinates” file; all other files contain the data in the file title. Detailed methods are in the submitted manuscript. A companion data package contains root trait data collected simultaneously from the same plots (Fraterrigo and Chen, 2020). See the "Related references" section for more information.2023/07/20 Update: The latest version of this dataset publication is version 2.0. The latest version of the data package was updated to correct the leaf size trait.csv file.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

MACCS (MELCOR Accident Consequence Code System) User Guide -- Version 4.0

The MELCOR Accident Consequence Code System (MACCS) is used by Nuclear Regulatory Commission (NRC) and various national and international organizations for probabilistic consequence analysis of nuclear power accidents. This User Guide is intended to assist analysts in understanding the MACCS/WinMACCS model and to provide information regarding the code. This user guide version describes MACCS Version 4.0. Features that have been added to MACCS in subsequent versions are described in separate documentation. This User Guide provides a brief description of the model history, explains how to set up and execute a problem, and informs the user of the definition of various input parameters and any constraints placed on those parameters. This report is part of a series of reports documenting MACCS. Other reports include the MACCS Theory Manual, MACCS Verification Report, Technical Bases for Consequence Analyses Using MACCS, as well as documentation for preprocessor codes including SecPop, MelMACCS, and COMIDA2.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Hydrogen Plus Other Alternative Fuels Risk Assessment Models (HyRAM+) Version 4.1 Technical Reference Manual

The HyRAM+ software toolkit provides a basis for conducting quantitative risk assessment and consequence modeling for hydrogen, methane, and propane systems. HyRAM+ is designed to facilitate the use of state-of-the-art models to conduct robust, repeatable assessments of safety, hazards, and risk. HyRAM+ integrates deterministic and probabilistic models for quantifying accident scenarios, predicting physical effects, characterizing hazards (thermal effects from jet fires, overpressure effects from delayed ignition), and assessing impacts on people. HyRAM+ is developed at Sandia National Laboratories to support the development and revision of national and international codes and standards, and to provide developed models in a publicly-accessible toolkit usable by all stakeholders. This document provides a description of the methodology and models contained in HyRAM+ version 4.1. The two most significant changes for HyRAM+ version 4.1 from HyRAM+ version 4.0 are direct incorporation of unconfined overpressure into the QRA calculations and modification of the models for cryogenic liquid flow through an orifice. In QRA mode, the user no longer needs to input peak overpressure and impulse values that were calculated separately; rather, the unconfined overpressure is estimated for the given system inputs, leak size, and occupant location. The orifice flow model now solves for the maximum mass flux through the orifice at constant entropy while conserving energy, which does not require a direct speed of sound calculation. This does not affect the mass flow for all-gaseous releases; the method results in the same speed of sound for choked flow. However, this method does result in a higher (and more realistic) mass flow rate for a given leak size for liquid releases than was previously calculated.

08 HYDROGEN↗

DOE OSTI2022

MACCS (MELCOR Accident Consequence Code System) User Guide Version 4.0, Revision 1

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

MCNP ® Code Version 6.3.0 Theory & User Manual

This document acts as a repository of knowledge for the Monte Carlo N-Particle (MCNP) transport computer code. It is maintained alongside the source code and attempts to introduce new users and re-familiarize experienced users with the theory and practices of using the MCNP code for the wide range of particle transport analyses that it is appropriate for. The latest version of the MCNP code, version 6.3.0, provides the Monte Carlo particle transport community with the latest feature developments and bug fixes in the MCNP code. The MCNP code version 6.0 and later is also known as the MCNP6 code.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2023

SAS4A/SASSYS-1 Version 5.7 and 5.6 Release Notes

SAS4A/SASSYS-1 (SAS) is a simulation tool used to perform deterministic analyses of anticipated events as well as design basis and beyond design basis accidents for advanced liquid-metal-cooled nuclear reactors. In this report, the major developments that were implemented in Versions 5.7 and 5.6 are summarized and an overview of all changes made between versions is presented. SAS Version 5.7 and 5.6 introduced a number of modeling improvements that allow users to capture important phenomena, such as pump heating and metallic fuel performance.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

ARM data-oriented metrics and diagnostics package for climate model evaluation (ARM-DIAGS-V3) version 3

A Python-based metrics and diagnostics package is currently being developed by the ARM Infrastructure Team at Lawrence Livermore National Laboratory to facilitate the use of long-term high frequency measurements from the ARM program in evaluating the regional climate simulation of clouds, radiation, precipitation, and aerosols. This metrics and diagnostics package computes climatological means of targeted climate model simulation and generates tables and plots for comparing the model simulation with ARM observational data. The CMIP model data sets are also included in the package to enable model inter-comparison as demonstrated in Zhang et al. (2018) and Zhang et al. (2020). The mean of the CMIP model can be served as a reference for individual models. Basic performance metrics are computed to measure the accuracy of mean state and variability of climate models. The evaluated physical quantities include cloud fraction, temperature, relative humidity, cloud liquid water path, total column water vapor, precipitation, sensible and latent heat fluxes, aerosol optical depth, and radiative fluxes, with plan to extend to more fields, such as the evaluation of model simulated aerosol physicochemical properties and cloud microphysics properties. Process-oriented diagnostics focusing on aerosol, cloud, and precipitation-related phenomena are also being developed for the evaluation and development of specific model physical parameterizations. In addition to the Southern Great Plains (SGP), North Slope of Alaska (NSA) and Tropical Western Pacific (TWP) atmospheric observatories in the ARMDIAGS version 2.0, the version 3.0 package have extended to the data collected at the ARM Eastern North Atlantic (ENA) atmospheric observatory and the Observation and Modeling of the Green Ocean Amazon (GOAMAZON) field campaign. The metrics and diagnostics package are currently built upon standard Python libraries and additional Python packages developed by DOE (CDAT). The ARM metrics and diagnostic package is available publicly with the hope that it can serve as an easy entry point for climate modelers to compare their models with ARM data. In this report, we first provide an overview of major metrics in section 2. The input data, which constitutes the core content of the metrics and diagnostics package, is summarized in section 3. A user's guide documenting the workflow/structure of the version 3.0 codes and including step-by-step instruction for running the package is described in section 4.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Hydrogen Plus Other Alternative Fuels Risk Assessment Models (HyRAM+) Version 5.1 Technical Reference Manual

The HyRAM+ software toolkit provides a basis for conducting quantitative risk assessment and consequence modeling for hydrogen, natural gas, and autogas systems. HyRAM+ is designed to facilitate the use of state-of-the-art models to conduct robust, repeatable assessments of safety, hazards, and risk. HyRAM+ integrates deterministic and probabilistic models for quantifying leak sizes and rates, predicting physical effects, characterizing hazards (thermal effects from jet fires, overpressure effects from delayed ignition), and assessing impacts on people. HyRAM+ is developed at Sandia National Laboratories to support the development and revision of national and international codes and standards, and to provide developed models in a publicly-accessible toolkit usable by all stakeholders. This document provides a description of the methodology and models contained in HyRAM+ version 5.1. The most significant changes for HyRAM+ version 5.1 from HyRAM+ version 5.0 are updated default leak frequency values for propane, new default component counts for different fuel types, and an improved fuel specification view in the graphical user interface.

02 PETROLEUM↗