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DOE OSTI2022

kynema-fmb [SWR-23-07]

Kynema-FMB (FKA: Kynema) is an open-source performance portable flexible multibody (FMB) dynamics solver designed for time-domain simulations. While originally tailored for wind turbine structural dynamics, the formulation and implementation are those of a general flexible-multidbody dynamics solver that can readily be applied to a wide range of systems. Kynema was designed with a narrow focus, namely to provide a lightweight, fast, accurate FMD solver for coupling to computational-fluid-dynamics (CFD) codes, especially the CFD codes in the Kynema suite, for fluid-structure-interaction (FSI) simulations. Kynema-FMB is equipped to model systems that can be represented as a collection of beams and rigid bodies that are connected through constraints. Degrees of freedom are defined in the inertial/global frame of reference and include displacements and rotations (formally as rotation matrices, but stored as quaternions). The underlying formulation is built on a Lie-group time integrator designed for index-3 differential-algebraic equations, which is second-order accurate in time (Bruls et al., 2012). Beam models are based on geometrically exact beam theory and are discretized as high-order spectral finite elements similar to those in BeamDyn (Wang et al., 2017). The governing equations for a FMD system like a wind turbine constitute a highly nonlinear system of constrained partial-differential equations. Kynema-FMB uses analytical Jacobians in the nonlinear-system solves in each time step. Linear systems use sparse storage and several third-party sparse-linear-system solvers are enabled. Ill conditioning of linear systems is mitigated with preconditioning described in Bottasso et al, 2008. Kynema-FMB is integrated with a simple open-source controller (ROSCO). There is an application programming interface (API) for coupling to geometry-resolved CFD (like that in Sharma et al., 2023) and actuator-force CFD (like that in Kuhn et al., 2025). In the latter, for actuator-line models, Kynema-FMB includes an internal blade-element solver that depends on user-provided lookup tables for coefficients of lift and drag, i.e., aerodynamic polars. Kynema-FMB is written in C++ and leverages Kokkos and Kokkos-Kernels (KokkosEcosystem) as its performance portability layer enabling simulations on both CPU and GPU systems. The repository is equipped with extensive automated testing at the unit and regression/system levels. The following describes the high-level development objectives conceived for Kynema: *Kynema will follow modern software development best practices, including test-driven development (TDD), version control, hierarchical automated testing, and continuous integration (CI) for a robust development environment. *The core data structures are memory efficient and enable vectorization and parallelization at multiple levels. *Data structures are data-oriented to exploit methods for accelerated computing including high utilization of chip resources (e.g., single instruction multiple data (SIMD) instruction sets) and parallelization using GP-GPUs. *The computational algorithms incorporate robust open-source libraries for mathematical operations, resource allocation, and data management. *The API design considers multiple stakeholder needs and ensure integration with existing and future ecosystems for data science, machine learning, and AI. *Kynema-FMB is written in modern C++ and leverages Kokkos as its performance-portability library with inspiration from the kynema stack.

Sprague, MichaelA.↗

DOE OSTI2026

Methods for evaluation and treatment of data shift

This is a code repository for a set of tools for detecting and mitigating data shifts in machine learning. The goal of the tools is to provide capabilities for determining when new data sets differ from training data sets and for adapting existing models to new data or correcting data shifts (via domain adaptation). The components will be written in Python, a high-level programming language that takes advantage of the Python ecosystem of high-quality open-source packages for machine learning and signal processing.

Parikh, Nidhi↗

DOE OSTI2022

An initial investigation of accuracy required for the identification of small molecules in complex samples using quantum chemical calculated NMR chemical shifts

The majority of primary and secondary metabolites in nature have yet to be identified, representing a major challenge for metabolomics studies that currently require reference libraries from analyses of authentic compounds. Using currently available analytical methods, complete chemical characterization of metabolomes is infeasible for both technical and economic reasons. For example, unambiguous identification of metabolites is limited by the availability of authentic chemical standards, which, for the majority of molecules, do not exist. Computationally predicted or calculated data are a viable solution to expand the currently limited metabolite reference libraries, if such methods are shown to be sufficiently accurate. For example, determining nuclear magnetic resonance (NMR) spectroscopy spectra in silico has shown promise in the identification and delineation of metabolite structures. Many researchers have been taking advantage of density functional theory (DFT), a computationally inexpensive yet reputable method for the prediction of carbon and proton NMR spectra of metabolites. However, such methods are expected to have some error in predicted 13 >C and 1 H NMR spectra with respect to experimentally measured values. This leads us to the question–what accuracy is required in predicted 13 C and 1 H NMR chemical shifts for confident metabolite identification? Using the set of 11,716 small molecules found in the Human Metabolome Database (HMDB), we simulated both experimental and theoretical NMR chemical shift databases. We investigated the level of accuracy required for identification of metabolites in simulated pure and impure samples by matching predicted chemical shifts to experimental data. We found 90% or more of molecules in simulated pure samples can be successfully identified when errors of 1 H and 13 C chemical shifts in water are below 0.6 and 7.1 ppm, respectively, and below 0.5 and 4.6 ppm in chloroform solvation, respectively. In simulated complex mixtures, as the complexity of the mixture increased, greater accuracy of the calculated chemical shifts was required, as expected. However, if the number of molecules in the mixture is known, e.g., when NMR is combined with MS and sample complexity is low, the likelihood of confident molecular identification increased by 90%.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Ferrite Specification for the Mu2e 300 kHz and 4.4 MHz AC Dipole Magnets

The Mu2e experiment at Fermilab will measure the rate for neutrinoless-conversion of negative muons into electrons with never-before-seen precision. This experiment will use a pulsed 8 GeV proton beam with pulses separated by 1.7 µs. To suppress beam induced backgrounds to this process, a set of dipoles operating at 300 kHz and 4.4 MHz have been developed that will reduce the fraction of out-of-time protons at the level of 1E-10 or less. Selection of magnetic ferrite material for construction must be carefully considered given the high repetition rate and duty cycle that can lead to excess heating in conventional magnetic material. A model of the electromagnetic and thermal properties of candidate ferrite materials has been constructed. Magnetic permeability, inductance, and power loss were measured at the two operating frequencies in toroidal ferrite samples as well as in the ferrites from which prototype magnets were built. Additionally, the outgassing rates of the ferrite material was measured to determine vacuum compatibility. The outcome of this work is a detailed specification of the electrical and mechanical details of the ferrite material required for this application.

43 PARTICLE ACCELERATORS↗

DOE OSTI2021

Picking an Open Source License at LLNL: Guidance and Recommendations from the Computing Directorate

Science and innovation are at the core of LLNL’s mission, and open source software is a vehicle by which LLNL innovations reach the scientific community, the nation, and the world. It also serves as a vehicle for building collaborations, publicizing our capabilities, and attracting new employees. Over half of the software produced by LLNL is open source, and open source licenses are the legal tools that allow our software to be used widely. Choosing an appropriate license can be difficult, but it can be even more difficult to change licenses after your software has amassed a significant number of contributors, so it is important understand the potentially subtle implications of your license choice. This document provides a set of recommendations for the busy and uninitiated. They are not set in stone (there are always exceptions). Our goal is to provide default choices that align best with LLNL’s mission, along with a high-level rationale.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2022

Ellipsoidal Fitting Methodology for Defect Clusters in Gallium Arsenide

In assessing the initial spatial distribution of defects from neutron or heavy ion irradiation, it is useful to have a reliable, automated, and fast-running tool to evaluate characteristic metrics such as the number of sub-clusters or the overall cluster volume. The latter metric, for instance, can be utilized to estimate a reference neutron fluence level at which inter-cluster interaction effects begin to become significant. This paper details a methodology to fit an arbitrarily complex defect map with a set of ellipsoids (one per identified sub-cluster) in which the constituent defects of a sub-cluster are determined using fuzzy degree-of-membership analysis. Specifically, a parameterized model is developed for point defects in gallium arsenide. Cluster volume calculations based on the model are compared against convex hull and single- ellipsoid representations. Results show that the parameterized sub-cluster model begins to deviate from the two reference models at a recoil energy of about 100 keV in GaAs, with the convex hull and single-ellipsoid representations increasingly overestimating the volume thereafter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Efficient and Selective Chemical Transformations in Highly Charged and Confined Nanodroplets

The acceleration of chemical reaction rates and the increased product selectivity in microdroplets compared to that in bulk solutions has become a topic of increasing interest that has been extensively characterized by electrospray ionization mass spectrometry (ESI-MS). However, the sources of this acceleration and the detailed relationships between droplet properties and resulting reaction rate acceleration are still under debate. Moreover, droplet properties are governed by multiple interrelated experimental parameters, i.e., electrospray voltage, solution flow rate, etc., which makes it difficult and time-consuming to explore this diverse parameter space using traditional manual experimental or computational approaches. In this work, we developed an automated experimental platform integrating reactions in controlled charged microdroplet environments with ESI-MS characterization and sequential hybrid Bayesian modeling, as well as an optimal experimental design framework, to achieve multidimensional parameter optimization for higher reaction turnover rates, based on a model reaction of tetraethylenepentamine (TEPA) with carbon dioxide. With the current platform, we have achieved automated scans with a range of electrospray voltages and solution flow rates, and determined and optimized parameter settings to achieve increased reaction turnovers. We have also linked this platform to the underlying properties of droplets via a hybrid model incorporating physics, high-level theoretical calculations, and machine learning (ML) approaches. The autonomous platform is broadly applicable to a range of chemical reactions relevant to DOE’s mission in chemical separations, catalysis, and materials synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

AWAKEN Site A1 - NREL Ceilometer (Vaisala CL51) / Derived Data

Site A1 netCDF L3 data files have level 3 (L3) data that have gone through the calculation service and contain all the data from the algorithms, including mixing layer height values and quality index data. L3 default files contain L3 data that use the default preset for a live plot. File naming schema: L3_DEFAULT_ _YYYYMMDDHHMM_ _ .nc Name Description L3 Identification of the data level DEFAULT Identification of the L3 file type CUSTOM OFFLINE STATION_NUMBER WMO station number, if defined YYYYMMDDHHMM UTC time ParameterKey Identification of the advanced algorithm settings. See the table below for an explanation. FREE_FORMAT File suffix, if defined

17 WIND ENERGY↗

DOE OSTI2023

WFIP3 - BARG site - NREL Ceilometer (Vaisala CL51) / Derived Data

17 WIND ENERGY↗

DOE OSTI2023

WFIP3 - BARG site - NREL Ceilometer (Vaisala CL51) / Derived Data

BARG ceilometer: netCDF L3 data files have level 3 (L3) data that have gone through the calculation service and contain all the data from the algorithms, including mixing layer height values, and quality index data. L3 default files contain L3 data that use the default preset for a live plot. File naming schema: L3_DEFAULT_ _YYYYMMDDHHMM_ _ .nc Name Description L3 Identification of the data level DEFAULT Identification of the L3 file type CUSTOM OFFLINE STATION_NUMBER WMO station number, if defined YYYYMMDDHHMM UTC time ParameterKey Identification of the advanced algorithm settings. See the table below for an explanation. FREE_FORMAT File suffix, if defined

17 WIND ENERGY↗

DOE OSTI2025

WFIP3 - NOAA SHIP site - NREL Ceilometer (Vaisala CL51) / Derived Data

NOAA SHIP ceilometer: netCDF L3 data files have level 3 (L3) data that have gone through the calculation service and contain all the data from the algorithms, including mixing layer height values, and quality index data. L3 default files contain L3 data that use the default preset for a live plot. File naming schema: L3_DEFAULT_ _YYYYMMDDHHMM_ _ .nc Name Description: L3 Identification of the data level DEFAULT Identification of the L3 file type CUSTOM OFFLINE STATION_NUMBER WMO station number, if defined YYYYMMDDHHMM UTC time ParameterKey Identification of the advanced algorithm settings. See the table below for an explanation. FREE_FORMAT File suffix, if defined

17 WIND ENERGY↗

DOE OSTI2025

WFIP3 - CACO site - NREL Ceilometer (Vaisala CL51) / Derived Data

CACO ceilometer: netCDF L3 data files have level 3 (L3) data that have gone through the calculation service and contain all the data from the algorithms, including mixing layer height values, and quality index data. L3 default files contain L3 data that use the default preset for a live plot. File naming schema: L3_DEFAULT_ _YYYYMMDDHHMM_ _ .nc Name Description: L3 Identification of the data level DEFAULT Identification of the L3 file type CUSTOM OFFLINE STATION_NUMBER WMO station number, if defined YYYYMMDDHHMM UTC time ParameterKey Identification of the advanced algorithm settings. See the table below for an explanation. FREE_FORMAT File suffix, if defined

17 WIND ENERGY↗

DOE OSTI2020

MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Collisional Excitation and Non-LTE Modeling of Interstellar Chiral Propylene Oxide

Abstract The first set of theoretical rotational cross sections for propylene oxide (CH 3 CHCH 2 O) colliding with cold He atoms has been obtained at the full quantum level using a high-accuracy potential energy surface. By scaling the collision reduced mass, rotational rate coefficients for collisions with para-H 2 are deduced in the temperature range 5–30 K. These collisional coefficients are combined with radiative data in a non-LTE radiative transfer model in order to reproduce observations of propylene oxide made toward the Sagittarius B2(N) molecular cloud with the Green Bank and Parkes radio telescopes. The three detected absorption lines are found to probe the cold (∼10 K) and translucent ( n H ∼ 2000 cm −3 ) gas in the outer edges of the extended Sgr B2(N) envelope. The derived column density for propylene oxide is N tot ∼ 3 × 10 12 cm −2 , corresponding to a fractional abundance relative to total hydrogen of ∼2.5 × 10 −11 . The present results are expected to help our understanding of the chemistry of propylene oxide, including a potential enantiomeric excess, in the cold interstellar medium.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

When Spectral Modeling Meets Convolutional Networks: A Method for Discovering Reionization-era Lensed Quasars in Multiband Imaging Data

Over the last two decades, around 300 quasars have been discovered at z ≳ 6, yet only one has been identified as being strongly gravitationally lensed. We explore a new approach—enlarging the permitted spectral parameter space, while introducing a new spatial geometry veto criterion—which is implemented via image-based deep learning. We first apply this approach to a systematic search for reionization-era lensed quasars, using data from the Dark Energy Survey, the Visible and Infrared Survey Telescope for Astronomy Hemisphere Survey, and the Wide-field Infrared Survey Explorer. Our search method consists of two main parts: (i) the preselection of the candidates, based on their spectral energy distributions (SEDs), using catalog-level photometry; and (ii) relative probability calculations of the candidates being a lens or some contaminant, utilizing a convolutional neural network (CNN) classification. The training data sets are constructed by painting deflected point-source lights over actual galaxy images, to generate realistic galaxy–quasar lens models, optimized to find systems with small image separations, i.e., Einstein radii of θ E ≤ 1''. Visual inspection is then performed for sources with CNN scores of P lens > 0.1, which leads us to obtain 36 newly selected lens candidates, which are awaiting spectroscopic confirmation. These findings show that automated SED modeling and deep learning pipelines, supported by modest human input, are a promising route for detecting strong lenses from large catalogs, which can overcome the veto limitations of primarily dropout-based SED selection approaches.

High-redshift galaxies↗

DOE OSTI2020

Frequency threshold determination for frequency-responsive load controllers

Systems, methods, and computer media for managing frequency response in a power grid are provided herein. Individual grid-connected electrical devices can be turned on and/or off by corresponding frequency-responsive load controllers when frequency deviations beyond a threshold are detected. Each controller selects, for the corresponding electrical device, a frequency threshold from available frequencies in a frequency range. If the selected frequency falls within a deadband frequency range, then the controller sets the frequency threshold to a frequency outside of the deadband (e.g., to a closest available frequency outside of the deadband). On a system-wide level, this approximates a uniform distribution of frequency thresholds over the entire frequency range, including the deadband, and achieves the proper power-to-frequency relationship for grid stability. A supervisory coordinator can determine the frequency range from which a frequency threshold is selected based on aggregated power information for devices and controllers throughout the grid.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Custom Accessors: Enabling Scalable Data Ingestion, (Re-)Organization, and Analysis on Distributed Systems

The emerging class of high velocity and high volume data analytic workflows comprise interwoven data ingestion, organization, and processing stages, with ingestion and organization steps often contributing comparable or even higher computational costs than actual processing steps. Since complex workflows consist of a variety of phases that view and use data differently, being able to construct efficient, scalable, distributed data structures (arrays, vectors, sets, maps, and multi-maps) is essential and requires custom methods to extend and shrink containers, analyze and position data, and, maintain globallyconsistent meta-data. In this paper, we propose a novel datastructure access paradigm based on the concept of Accessors. At a high level, accessors are customizable callable objects that can modify the behavior of insert, read, update, and delete operations for distributed containers while preserving atomicity guarantees. Accessors provide a very clean and natural way to implement a variety of programming patterns, e.g., conditional insertion/deletion and cascading computations, which would be otherwise hard (or even impossible) to express in parallel and distributed settings without using locks. We demonstrate the practicality and usefulness of our approach with two representative use cases and study the performance of these applications on a distributed High-Performance Computing system. Our analysis highlights that our proposed abstraction allows for an effective overlapping and concurrent execution of different workflow steps (e.g., data ingestion and analysis), which in a conventional analytics pipeline would execute sequentially, contributing cumulatively to the overall latency.

Castellana, Vito G. [BATTELLE (PACIFIC NW LAB)] (O↗

DOE OSTI2020

Radar Derived Rainfall and Rain Gauge Measurements at SRS

Over the years rainfall data for the Savannah River Site has been obtained from ground level measurements made by rain gauges. These instruments have inherent errors or biases that can impact the measured rainfall totals but are assumed as ground truth for most climatological and weather applications. With the development of weather radar technologies, various methods to derive rainfall totals from radar reflectivity values have been developed and have continued to improve. The Z-R relationship, which uses an exponential relationship to estimate rainfall rate based on radar reflectivity values, provides estimates of rainfall amounts (Z-R Level III) for locations within the radar’s detection range. The recently developed Multi-Radar Multi-Sensor (MRMS) dataset combines reflectivity-based estimates using the Z-R relationship with a network of gauges and other rainfall estimates to produce a refined set of precipitation estimates for each grid point within its domain. Comparisons were done between gauge observations and radar estimates for various SRS locations to assess whether radar derived estimates are representative of rainfall measurements at the site. Results obtained show good agreement between radar derived amounts and ground measurements, with MRMS showing stronger correlations and lower spread than Z-R Level III estimates. Outliers and errors observed appear to be related to hydrometeor classification schemes. In general, MRMS proved to provide sufficiently representative estimates of daily rainfall amounts to replace existing SRS rain gauge measurements.

54 ENVIRONMENTAL SCIENCES↗