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All sources NASA NTRS DOE OSTI

DOE OSTI2021

The Polar System Analysis Package (Ver. 1 Specifications)

The Polar System Analysis Package (POLeSTAr) is a modern data fusion tool being designed to benchmark,evaluate and compare the polar physics and biogeochemistry of Earth System Models (ESMs). It is being written in Python to make use of libraries including Xarray, Matplotlib, SciPy, NumPy and PyTorch within algorithms developed specifically for polar system modeling. Initial POLeSTAr algorithms will be adapted from the MATLAB Ridgepack package that was designed to analyze the Model for Prediction Across Scales (MPAS) sea ice component of the Energy Exascale Earth System Model (E3SM) and sea ice model CICE within the Community Earth System Model (CESM).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Batched Sparse Linear Algebra (Final Report for Subcontract B648960)

This report finalizes design specifications for developing batched kernels for small tensor operations for unassembled matrix-free iterative solvers, batched solvers for partially assembled operators, and batched solvers with support for various sparse formats. The outcome of the project milestones is a set of interfaces to Batched Sparse LA solvers running on hardware accelerators for use in ECP Libraries and Applications. It is part of the development of sparse batched kernels, solvers/preconditioners as well as creating interoperability in xSDK libraries with sparse and dense batched functions to benefit ECP applications. The participants included representatives from ECP libraries (not limited to the xSDK project), applications, and vendors (AMD, Intel, and NVIDIA). Batched sparse linear algebra solvers form the new frontier for algorithmic development and performance engineering. Many applications (ECP and non-ECP alike) require simultaneous solutions of small linear systems of equations that are structurally sparse. To move towards high hardware utilization, it is important to provide these applications with appropriate interfaces to efficient batched sparse solvers running on modern hardware accelerators. We present interface designs in use by HPC software libraries supporting batched sparse linear algebra and the development of sparse batched kernel codes for solvers and preconditioners. We also address the potential interoperability opportunities to keep the software portable between the major hardware accelerators from AMD, Intel, and NVIDIA. The presented interface specifications includes batched band, sparse iterative, and sparse direct solvers. This report summarizes progress in Kokkos Kernels and the xSDK libraries MAGMA, Ginkgo, hypre, SUNDIALS, and SuperLU_dist.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

An in silico method to assess antibody fragment polyreactivity

Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. Here, we design a set of experiments using a diverse naïve synthetic camelid antibody fragment (nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally test our models’ performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the models allow us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its functional properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Retrofit Energy Analysis and Central Thermal modeling (REACT) v1.0

REACT is a website designed to simplify the analysis and decision-making process for retrofitting existing central plant heating and cooling systems with advanced heat pump technologies. The tool evaluates the technical and economic viability of replacing traditional boilers with various options including water-to-water or air-to-water heat pumps, which can provide efficient and lower-cost heating and cooling. It allows users to compare current central plant configurations with retrofit scenarios, assessing energy consumption, life-cycle costs, and environmental impact. Retrofitting traditional boiler and chiller systems with water-to-water or air-to-water heat pumps can significantly reduce energy consumption and lower lifecycle costs. The REACT provides: User-Friendly Tools: A user friendly web interface for quick, intuitive analysis accessible to non-experts. Advanced Modeling: A Python-powered engine for detailed parametric studies, optimization, and research applications. Comprehensive Analysis: Lifecycle cost evaluation, energy consumption modeling, and environmental impact assessment. Visual Insights: A variety of plots to visualize system performance and design trade-offs. The engine for the website (REACT) bases on several Python libraries, and the website will be hosted on an ETA server.

Kim, Donghun [Lawrence Berkeley National Laborator↗

DOE OSTI2021

Multilevel Training of Neural Networks

MTNN is a software library for applying multilevel algorithms on training neural networks. Based on PyTorch, it is designed to be an extensible framework to enable researchers to implement multilevel training algorithms on a variety of neural network models. This release includes a culmination of preliminary work in applying the multilevel Full Approximation Scheme technique on fully connected and convolutional neural networks to solve PDE problems (pending publication submission).

Li, Ruipeng↗

DOE OSTI2024

Mu2e experiment: Simulation of the Production Target

The Mu2e experiment will search for coherent, neutrinoless conversion of muons to elections in an aluminum stopping target. A simulation program is used to experiment and design the production target of the Mu2e experiment. The module uses programing languages and libraries to work. The program called the Offline uses C++ as the programing language in the module. To construct the simulation, the Geant4 library constructs shapes and uses them in the simulation program, ROOT. The offline program simplifies the creation of the tube by organizing them into parameter objects and nesting them with other variables required to construct the tube-like center point, material, or if it is allowed to conflict with other solids. The parameter varies for every solid tube. The geometry file uploads the parameters by declaring and organizing the parameters in C++ using the configuration tools. The author describes the development and the future of this project.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Mu2e experiment: Simulation of the Production Target

Szewczyk, Albert↗

DOE OSTI2021

Design of multi-scale protein complexes by hierarchical building block fusion

A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Accelerating Low-Income Financing and Transactions (LIFT) for Solar Access Everywhere (Final Technical Report)

The Accelerating Low-Income Financing and Transactions (LIFT) for Solar Access Everywhere project’s goal was to expand Low-to-Moderate Income (LMI) solar access for homeowners and renters. The LIFT project researched and gathered data on 453 LMI community solar project across the country. Following three years of research, the project delivered three groundbreaking research papers in June 2022, focused on 1) customer experience, 2) the growth of community solar programs, and 3) project-level financial best practices for serving LMI communities. These were followed by a user-friendly web-based Toolkit allowing users to interact with project data and key findings in November 2022. The customer experience research examined community solar subscribers’ primary motivations to join and remain satisfied with projects. Our research identified 453 projects across the country that dedicated some portion of the system capacity to LMI households. Seventeen of these projects participated in the LIFT customer experience research, allowing the project team to survey their customers and gain insight into how LMI subscribers feel about community solar and the programs that serve them. Subscribers in our sample indicated that the most critical issue that motivated them to participate in their program, however, was not savings but helping the environment. This was true for both LMI and non-LMI subscribers. Helping the environment was also the most important issue for LMI subscribers to measure how well their program was working for them. LIFT also explored how rapidly community solar has grown since its inception in 2006, publishing results in the Growth of U.S. Community Solar Serving LMI Households report. The results showed that community solar projects serving LMI households are one of the fastest growing segments of the solar industry. The report identifies and recommends ways developers should overcome real or perceived risks to LMI customer acquisition and subscriber management. Through the analysis of community solar project finance research, LIFT showed that most community solar projects serving LMI households are financed in the same ways mainstream community solar projects are financed. The value stacks and financial returns are no different, although LMI inclusion and participation rate varied across programs in our sample, ranging from between 10% and 100%. Based on the findings from the LIFT research, the team built a web-based user-friendly Toolkit, consisting of case studies, project finance best practices, and several tools built around the national dataset of 453 community solar projects that serve LMI households. These allow users to engage with the dataset in multiple ways; to explore the landscape of LMI community solar in the U.S., and to design community solar projects to optimize LMI inclusion, equity, and savings levels. The Toolkit also includes a library of LIFT-generated and LIFT-curated resources for users to learn more about how to best serve LMI communities through community solar. LIFT officially published the Toolkit on October 31, 2022, followed by a launch event (public webinar) on November 17, 2022. The core LIFT partners continue to engage in outreach and dissemination efforts to promote the LIFT Toolkit and research publications. Our driving motivation is to continue enabling solar developers to leverage the findings of this three-year research effort. By implication, the LIFT Toolkit is designed for use by utilities, energy service providers, and financiers or investors as a learning and decision-making tool to rapidly scale project models that optimize LMI inclusion and maximize real household savings.

14 SOLAR ENERGY↗

DOE OSTI2021

Functional Requirements for the WEIS Toolset to Enable Controls Co-Design of Floating Offshore Wind Turbines

The goal of the new Wind Energy with Integrated Servo-control (WEIS) toolset under development is to provide the offshore wind industry and research communities with an open-source, user-friendly, flexible tool to enable true controls co-design (CCD) of the physical design of a floating offshore wind turbine together with the controller. WEIS will use a multifidelity library of models built on the foundations of WISDEM® and OpenFAST formerly known as FAST). This paper presents the WEIS development plan, including the functional requirements of WEIS (including improvements to WISDEM and OpenFAST) together with associated rationale for their establishment and a qualitative description of the modeling approaches that will be implemented to address these functional requirements. The development of WEIS is a project under the Aerodynamic Turbines Lighter and Afloat with Nautical Technologies and Integrated Servo-control program funded by the U.S. Department of Energy Advanced Research Projects Agency – Energy.

27 ARPA - Advanced Research Projects Agency-Energy↗

DOE OSTI2024

HamLib: A library of Hamiltonians for benchmarking quantum algorithms and hardware

In order to characterize and benchmark computational hardware, software, and algorithms, it is essential to have many problem instances on-hand. This is no less true for quantum computation, where a large collection of real-world problem instances would allow for benchmarking studies that in turn help to improve both algorithms and hardware designs. To this end, here we present a large dataset of qubit-based quantum Hamiltonians. The dataset, called HamLib (for Hamiltonian Library), is freely available online and contains problem sizes ranging from 2 to 1000 qubits. HamLib includes problem instances of the Heisenberg model, Fermi-Hubbard model, Bose-Hubbard model, molecular electronic structure, molecular vibrational structure, MaxCut, Max- k -SAT, Max- k -Cut, QMaxCut, and the traveling salesperson problem. The goals of this effort are (a) to save researchers time by eliminating the need to prepare problem instances and map them to qubit representations, (b) to allow for more thorough tests of new algorithms and hardware, and (c) to allow for reproducibility and standardization across research studies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae

Antibiotic use can lead to the expansion of multi-drug-resistant pathobionts within the gut microbiome that can cause life-threatening infections. Selective alternatives to conventional antibiotics are in dire need. Here, in this work, we describe a Klebsiella PhageBank for the tailored design of bacteriophage cocktails to treat multi-drug-resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. pneumoniae, we identify host factors required for phage infection in major Klebsiella phage families. Leveraging the diversity of the PhageBank, we formulate phage combinations that eliminate K. pneumoniae with minimal phage resistance. Optimized cocktails selectively suppress the burden of K. pneumoniae in the mouse gut and drive the loss of key virulence factors that act as phage receptors. Phage-mediated diversification of bacterial populations in the gut leads to co-evolution of phage variants with higher virulence and broader host range. Altogether, the Klebsiella PhageBank charts a roadmap for phage therapy against a critical multidrug-resistant human pathogen.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

CLMM : a LSST-DESC cluster weak lensing mass modeling library for cosmology

ABSTRACT We present the v1.0 release of CLMM, an open source python library for the estimation of the weak lensing masses of clusters of galaxies. CLMM is designed as a stand-alone toolkit of building blocks to enable end-to-end analysis pipeline validation for upcoming cluster cosmology analyses such as the ones that will be performed by the Vera C. Rubin Legacy Survey of Space and Time-Dark Energy Science Collaboration (LSST-DESC). Its purpose is to serve as a flexible, easy-to-install, and easy-to-use interface for both weak lensing simulators and observers and can be applied to real and mock data to study the systematics affecting weak lensing mass reconstruction. At the core of CLMM are routines to model the weak lensing shear signal given the underlying mass distribution of galaxy clusters and a set of data operations to prepare the corresponding data vectors. The theoretical predictions rely on existing software, used as backends in the code, that have been thoroughly tested and cross-checked. Combined theoretical predictions and data can be used to constrain the mass distribution of galaxy clusters as demonstrated in a suite of example Jupyter Notebooks shipped with the software and also available in the extensive online documentation.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

WaterTAP v1.0.0

WaterTAP is a new open source library of water-specific models built on the IDAES Integrated Platform to support the design and optimization of integrated water treatment systems, improve existing systems and enable the analysis of new designs incorporating emerging technologies. WaterTAP enables advanced modeling and optimization for: conceptual and multiscale design, dynamics and model predictive control of water systems and networks.

Beattie, KeithS↗

DOE OSTI2020

Exascale-capable cellular automaton for nucleation and grain growth

This model is a cellular automata-based algorithm used to predict grain-scale microstructure development. Nucleation and growth of existing grains are considered in an initially liquid domain, where the temperature field evolution is either driven through heat transport simulation data or a frozen temperature approximation (i.e., a constant cooling rate and a fixed thermal gradient). The growth of grains is based on the decentered octahedron algorithm published by Gandin and Rappaz (https://doi.org/10.1016/S1359-6454(96)00303-5), where the grain envelopes are tracked as approximations of the evolving dendritic growth front. The input heat transport data, which can come from simulation of an arbitrary processing technique, consists of coordinates and times at which said coordinates fall below the liquidus and solidus temperatures for the final time. As a result, only the final solidification of a given region is modeled (no remelting). The code is designed to be compatible with pre-Exascale architectures, and uses MPI and the Kokkos library to decompose the computational domain and offload solidification calculations to GPUs.

Rolchigo, MatthewR.↗

DOE OSTI2020

Preliminary design analysis workflow for Division 5 HHA-3200 requirements for graphite core components

This report presents a design analysis workflow for graphite core components and assemblies, based on the design rules of ASME Boiler Pressure and Vessel Code, Section III, Division 5, Article HHA-3000. The workflow contains three stages: developing the design of the graphite core component, modeling the component with the finite element software MOOSE, and assessing if the component passes/fails the criteria of the HHA-3000 design rules. Since the design rules use probabilistic metrics specifically established to evaluate brittle materials, we developed a python library that performs all the statistical calculations necessary for the evaluations of the HHA-3000 criteria.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Orca2

SAND2024-03236O Orca2 is a trajectory design and optimization code for constructing and solving problems numerically defined on homogeneous manifolds. Orca2 solves numerical trajectory design and optimization problems defined on Lie-type domains and operates primarily as a library requiring a user to write additional C++ code to leverage it. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Sparapany, Michael↗

DOE OSTI2023

Parallel Runtime Interface for Fortran (PRIF) Design Document (Rev. 0.2)

This design document proposes an interface to support the parallel features of Fortran, named the Parallel Runtime Interface for Fortran (PRIF). PRIF is a proposed solution in which the runtime library is responsible for coarray allocation, deallocation and accesses, image synchronization, atomic operations, events, and teams. In this interface, the compiler is responsible for transforming the invocation of Fortran-level parallel features into procedure calls to the necessary PRIF procedures. The interface is designed for portability across shared- and distributed-memory machines, different operating systems, and multiple architectures. Implementations of this interface are intended as an augmentation for the compiler's own runtime library. With an implementation-agnostic interface, alternative parallel runtime libraries may be developed that support the same interface. One benefit of this approach is the ability to vary the communication substrate. A central aim of this document is to define a parallel runtime interface in standard Fortran syntax, which enables us to leverage Fortran to succinctly express various properties of the procedure interfaces, including argument attributes.

97 MATHEMATICS AND COMPUTING↗