Results for “Mathematical Software” — Page 61

DOE OSTI2021

SAM Theory Manual

The System Analysis Module (SAM) is an advanced and modern system analysis tool under development at Argonne National Laboratory for advanced non-LWR reactor safety analysis. It aims to provide fast-running, modest-fidelity, whole-plant transient analyses capabilities, which are essential for fast turnaround design scoping and engineering analyses of advanced reactor concepts. While SAM is being developed as a system-level modeling and simulation tool, advanced modeling techniques being implemented include a reduced-order three-dimensional module, pseudo 3-D conjugate heat transfer modeling in reactor core, flexible and multi-scale modeling of heat transfer between fluid and structures, in addition to the advances in software environments and design, and numerical methods. SAM aims to be a generic system-level safety analysis tool for advanced non-LWRs, including Liquid-Metal-cooled fast Reactors (LMR), Molten Salt Reactors (MSR), Fluoride-salt-cooled High- temperature Reactors (FHR), and High-Temperature Gas-cooled Reactors (HTGR). SAM takes ad- vantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented computational framework (MOOSE), and its underlying meshing and finite-element library and linear and non-linear solvers, to leverage the modern advanced software environments and numerical methods. This document provides the theoretical and technical basis of the code to help users understand the underlying physical models (such as governing equations, closure models, and component models), system modeling approaches, numerical discretization and solution methods, and the overall capabilities in SAM. As new code capabilities and features are added, the SAM Theory Manual will be updated periodically to keep it consistent with the state of the development.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Machine learning approaches for integrating multi-omics data to expand microbiome annotation

Preliminary: This final report corresponds to a grant (DE-SC0021216) that was awarded to the University of Montana. Mid-way through the grant period, I relocated from the University of Montana to the University of Arizona. The grant was ended at University of Montana in late 2022, with all efforts concluding on 08/26/22; the remaining funds supporting the project were relinquished by University of Montana, and were later awarded to University of Arizona under a new grant, with start date 04/01/23. This report focuses on results of research efforts at UMontana through 08/26/22. Results: We made progress in each of the three aims of the proposal. We released software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes. We made substantial progress in developing software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we made notable progress in developing AI methods (specifically: a neural embedding model) for identifying similarities between protein sequences based on amino-wise latent vectors. These efforts were supplemented by development of methods for protein modeling in support of predicting protein-drug binding activity, and by my leadership of a team in the NIH/DOE 2021 Petabyte-Scale Sequence Search hack-a-thon.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Simulation Process Automation for Window Attachments Rating

WINDOW (LBNL 2022) and AERCalc (LBNL 2018) software developed by Lawrence Berkely National Laboratory are needed for running the tool. The database that in installed along with WINDOW software is utilized and modified to develop database for AERCalc simulation in generic case. However, any other custom WINDOW database created by users can be utilized as well. Another requirement for use of the tool is the availability of the shading fabric in the complex glazing database (CGDB). The CGDB id of the fabric was used for database generation discussed in next section.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

V-HAMSTeR v1.0.0

V-HAMSTeR is a bioinformatics software tool designed to predict the hosts of viruses directly from genomic sequences. It can be used by researchers to predict animal, prokaryotic, plant, protist or fungal viral hosts including viruses that may be fragmented or discovered in environmental metagenomic datasets. Features & Uses: The software employs a novel dual-stream deep learning architecture that dynamically fuses implicit sequence embeddings from a genomic foundation model with 13 explicit, handcrafted biological features (e.g., coding density and strand switch rates). To ensure maximum reliability, V=HAMSTeR deploys a 5-fold deep ensemble calibrated via Joint Temperature Scaling, providing users with statistically rigorous confidence probabilities. It also features an automated sequence chunking and mean-pooling module to seamlessly process variable-length contigs. Advantages Over Similar Technologies: Existing tools (e.g., IPEV, RNAVirHost) typically rely on either basic k-mers or isolated neural networks. V-HAMSTeR's hybrid architecture captures both broad genomic context and specific biological motifs that standalone foundation models often miss. Furthermore, unlike competitor tools that struggle with incomplete data or exhibit extreme overconfidence, V-HAMSTeR is explicitly benchmarked and mathematically calibrated for fragmented assemblies (1kb–10kb). This makes it uniquely robust, accurate, and trustworthy for the messy reality of real-world environmental viromics.

Grigson, Susie [Lawrence Berkeley National Laborat↗

DOE OSTI2020

Treatment of Tilted Sonar Data for Salt Cavern Analysis

Structural modeling and visualization of salt caverns requires three-dimensional representations. These representations are typically produced from sonar surveys conducted by companies that then produce a report of depths, distances, and volumes. There are multiple formats that are vendor dependent, and, as technology improves, there have been changes from only horizontal surveys to inclined shots for ceilings and floors to mid-cavern inclined shots. For geomechanical modeling, leaching predictions, and cavern stability visualizations, Sandia has previously written in-house software, called SONAR8, that created a consistent geometry format from the processed sonar reports. However, the increase in the need for mid-cavern inclined surveys led to the discovery of certain limitations in that code. This report describes methods used to process the multiple different formats to handle inclined shots in a consistent and accurate manner in our modeling efforts. A set of file formats and a database schema that was developed for this work is also documented in the appendices.

02 PETROLEUM↗

DOE OSTI2020

OpenK: An Open Infrastructure for the Accumulation, Sharing and Reuse of High Performance Computing Knowledge

In high performance computing (HPC), often a wide range of knowledge about the particular domains, software applications, and hardware architectures are necessary for applying the right optimizations in the appropriate contexts. In today’s practice, however, such knowledge has been expressed and managed in an ad-hoc manner by each individual. Systematic accumulation, sharing and reuse of the knowledge across a broad community has been difficult. This paper introduces OpenK, an ontology-based open infrastructure for solving the problem. By centering around ontology – a generic knowledge representation – and extensible designs, it offers a promising support for lowering the barriers.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

More Tools for Visualization and Analysis of Small-Angle Neutron Scattering Data: Descriptions and Examples

With the adoption of drtsans as the data reduction software for the GP-SANS, Bio-SANS and EQ-SANS instruments at ORNL, tools for data visualization and analysis that can be integrated into drtsans scripts are needed to further improve the user experience. New tools that do not need to be incorporated directly into data reduction scripts can also positively impact users during their experiments. In this report, a new set of tools is presented that complements the previous set released. The set includes tools for both fitting data and for visualizing data.

42 ENGINEERING↗

DOE OSTI2024

Designing Cellular Metal Structures for Thermal Insulation

This project focused on developing topology optimization software to design advanced metal thermal insulators. Initially, solid designs were created that matched the thermal performance of current baseline designs but were significantly heavier. To address this, cellular materials were incorporated, specifically the octet structure which is known for its high strength-to-weight ratio and thermal properties. By leveraging these cellular designs at various densities, superior thermal and mechanical performance was achieved without added weight. This novel approach enhances thermal management and structural integrity under extreme conditions, offering promising advancements for thermal protection systems.

36 MATERIALS SCIENCE↗

DOE OSTI2021

FAST-1.0.1 User Installation and Verification Guide

The purpose of this document is to provide the user information about the installation of FAST-1.0.1 on their computers or servers. General information about the code and supported operating systems is described in Section 1.0.1. Self-service oriented FAST-1.0.1 software licensing steps are described in Section 2.0. An installation verification test suite is provided with FAST-1.0.1 and described in Section 3.0. A convenience script for converting FRAPCON to FAST inputs is discussed in Section 4.0. FAST-1.0.1 was developed and released under a software quality assurance program based upon NQA-1-2017. FAST-1.0.1 is the latest baseline code and the result of a bug fixes to FAST-1.0 with other software and methodology developments. The installation verification test suite contains both steady state and transient Anticipated Operation Occurrences (AOOs). Capability to model accident conditions, such as Reactivity Initiated Accidents (RIAs) and Loss Of Coolant Accidents (LOCAs), are targeted for a later release of FAST. FRAPTRAN-2.0 will continue to be used for accident conditions until the release of FAST with accident condition modeling capabilities.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Microgrid Design Toolkit (MDT) User Guide. Software v1.3.

The Microgrid Design Toolkit (MDT) supports decision analysis for new ("greenfield") microgrid designs as well as microgrids with existing infrastructure. The current version of MDT includes two main capabilities. The first capability, the Microgrid Sizing Capability (MSC), is used to determine the size and composition of a new, grid connected microgrid in the early stages of the design process. MSC is focused on developing a microgrid that is economically viable when connected to the grid. The second capability is focused on designing a microgrid for operation in islanded mode. This second capability relies on two models: the Technology Management Optimization (TMO) model and Performance Reliability Model (PRM).

42 ENGINEERING↗

DOE OSTI2022

Moving Target Defense Routing for SDN-enabled Smart Grid

The increasing attack surface area in the smart grid communication networks is making the grid more susceptible to cyber attacks that can lead to instability of the grid and even blackouts. While there are multiple types of cyber attacks that can impact the grid, Denial of Service (DoS) attacks are relatively easier to inject as they require lesser knowledge about the system as compared to data integrity attacks. Various research works showcase methods to prevent or mitigate the impacts of DoS attacks in the smart grid but the research still lacks in demonstrating the feasibility and efficacy of the solutions in a real-world environment. In this paper, we propose a Moving Target Defense (MTD)-enabled Software Defined Network (SDN) for the Smart Grid communication implemented on a Hardwarein- the-Loop (HIL) Testbed. We showcase the implementation of the proposed architecture of MTD-enabled SDN using Mininet 2.3.0 which enables communication between the physical grid and the control center. The results show the advantages of using MTD based on SDN for the wide-area network (WAN) with much lower packet drop percentages in the case of MTD-based routing in the SDN WAN. Index Terms—SDN,

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

FTK: A Simplicial Spacetime Meshing Framework for Robust and Scalable Feature Tracking

In this work, we present the Feature Tracking Kit (FTK), a framework that simplifies, scales, and delivers various feature-tracking algorithms for scientific data. The key of FTK is our simplicial spacetime meshing scheme that generalizes both regular and unstructured spatial meshes to spacetime while tessellating spacetime mesh elements into simplices. The benefits of using simplicial spacetime meshes include (1) reducing ambiguity cases for feature extraction and tracking, (2) simplifying the handling of degeneracies using symbolic perturbations, and (3) enabling scalable and parallel processing. The use of simplicial spacetime meshing simplifies and improves the implementation of several feature-tracking algorithms for critical points, quantum vortices, and isosurfaces. As a software framework, FTK provides end users with VTK/ParaView filters, Python bindings, a command line interface, and programming interfaces for feature-tracking applications. We demonstrate use cases as well as scalability studies through both synthetic data and scientific applications including tokamak, fluid dynamics, and superconductivity simulations. We also conduct end-to-end performance studies on the Summit supercomputer. FTK is open sourced under the MIT license: https://github.com/hguo/ftk.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Newly Released Capabilities in the Distributed-Memory SuperLU Sparse Direct Solver

We present the new features available in the recent release of SuperLU_DIST, Version 8.1.1. SuperLU_DIST is a distributed-memory parallel sparse direct solver. The new features include (1) a 3D communication-avoiding algorithm framework that trades off inter-process communication for selective memory duplication, (2) multi-GPU support for both NVIDIA GPUs and AMD GPUs, and (3) mixed-precision routines that perform single-precision LU factorization and double-precision iterative refinement. Apart from the algorithm improvements, we also modernized the software build system to use CMake and Spack package installation tools to simplify the installation procedure. Throughout the article, we describe in detail the pertinent performance-sensitive parameters associated with each new algorithmic feature, show how they are exposed to the users, and give general guidance of how to set these parameters. We illustrate that the solver’s performance both in time and memory can be greatly improved after systematic tuning of the parameters, depending on the input sparse matrix and underlying hardware.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.13 Theory Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Theory Manual (V.6.15)

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Deployable Wind-Hybrid Power Systems for Defense and Disaster Response Applications

This report presents an analysis of the performance of deployable energy systems comprised of wind energy systems integrated with diesel generators, photovoltaic systems, and battery storage to meet the load requirements of a representative U.S. Army forward operating base. The analysis is conducted using HOMER, a microgrid analysis software that can search through a wide range of parameters to design and optimize microgrid power systems. The search parameters include the system architecture, the wind and solar resources, and the availability of diesel fuel. The results of the analysis measure the relative performance of the different systems and environments in terms of the overall transportation cost to deploy the system and the ability to provide resilience in terms of meeting mission critical loads.

02 PETROLEUM↗

DOE OSTI2021

Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.16 Theory Manual

The Dakota toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quantification, and optimization under uncertainty that provide the foundation for many of Dakota’s iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Methods for Estimating Dose from Galactic Cosmic Rays and Jovian Radiation Belts on Reduced-Order Monte Carlo Geometries

This document outlines the methods and tools developed to estimate dose rates from galactic cosmic rays and the trapped radiation belts surrounding Jupiter using Monte Carlo particle transport software. Furthermore, the techniques described here are specific for translating high-resolution MAVRIC models to analogous but lower resolution Monte Carlo N-Particle Transport (MCNP) code models to estimate charged particle effects on models originally developed to study neutral particles only. This capability was initially developed to predict doses to various components of dynamic radioisotope power systems for spaceflight applications, but the tools and methods can be easily applied to other problem geometries and expanded to other space radiation environments.

79 ASTRONOMY AND ASTROPHYSICS↗