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DOE OSTI2021

The Utility in Conjoint Analysis as a Fast Expert Elicitation Technique

This paper presents an interface and analysis technique for quickly conducting expert elicitation with the goal of determining entity importance. Our interface deploys a two-alternative choice experiment that is capable of representing knowledge graphs in an easy to interpret fashion for users with limited experience with knowledge graphs. Our analysis methodology takes advantage of conjoint analysis techniques and provides entity weights for many SMEs simultaneously. The results largely align with individual participant fits.

Conjoint Analysis, interface, Expert Elicitation, ↗

DOE OSTI2025

Bridging the Gap Between Modern UX Design and Particle Accelerator Control Room Interfaces

Accelerator control systems often represent relatively complex and safety-sensitive human-machine interfaces within process control industries. These systems are technically robust and reflect the cumulative integration of solutions built and adapted across decades. One of the regular, unfortunate casualties of provisional accelerator control system updates is their human-system interfaces (HSIs) which often lag behind modern usability and design standards. An additional challenge is that although there is a multitude of established human factors (HF), and user experience (UX) principles for everyday digital applications, there are very few (if any) established principles for complex and safety-critical applications for an accelerator. This paper argues for the importance of established HF and UX principles (herein referred to as human-centered design principles) into the development of accelerator HSIs, emphasizing the need for clarity, consistency, responsiveness, and cognitive accessibility. Drawing from HF/UX best practices and human-centered design, this paper discusses how these approaches can enhance operator performance, reduce human error, and improve accelerator personnel collaboration. Case studies from Accelerator Control Operations Research Network (ACORN) at Fermilab are explored to demonstrate how interfaces built with human-centered design principles can scale with system complexity while remaining intuitive and efficient for diverse user roles including operators, machine experts, and engineers. By bridging the gap between traditional control system design and modern human-centered design methods, this paper provides a roadmap for evolving accelerator HSIs into more usable, maintainable, and effective tools.

Hill, Rachael [Idaho Natl. Lab.]↗

DOE OSTI2014

Metabolomic data streaming for biology-dependent data acquisition

During the last 10 years, metabolomics has emerged as a powerful technology to interrogate cellular biochemistry at the global level. Although much of the success has been driven by advances in mass spectrometry, developments in bioinformatic resources for data processing have been equally important. Additionally, the widely used metabolomic software XCMS, in particular, has undergone substantial improvements since its first introduction in 2005 (ref. 1). In addition to improved algorithms for peak picking, retention time alignment and data visualization, XCMS has transitioned from a command-line interface requiring expertise with the R programming language, to a web-based platform with a graphical user interface2. This web-based platform, which we call XCMS Online, enables thousands of users to upload their metabolomic data and perform cloud-based processing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Contact Control, Version 1

The contact control code is a generalized force control scheme meant to interface with a robotic arm being controlled using the Robot Operating System (ROS). The code allows the user to specify a control scheme for each control dimension in a way that many different control task controllers could be built from the same generalized controller. The input to the code includes maximum velocity, maximum force, maximum displacement, and a control law assigned to each direction and the output is a 6 degree of freedom velocity command that is sent to the robot controller.

von Sternberg, Alex↗

DOE OSTI2021

FIERRO V.X

FIERRO is a modern C++ code intended to simulate quasi-static solid mechanics problems and transient, compressible material dynamic problems with Lagrangian methods, which have meshes with constant mass elements that move with the material. FIERRO is designed to aid a) material model research that has historically been done using commercial implicit and explicit finite element codes, b) numerical methods research, and c) computer science research. FIERRO supports user developed material models that adhere to several industry standard formats by using a C++ to Fortran interface to couple the model to the numerical solvers. FIERRO is built on the ELEMENTS library that supports a diverse suite of element types, including high-order elements, and quadrature rules. The mesh class within the ELEMENTS library is designed for efficient calculations on unstructured meshes and to minimize memory usage. FIERRO is designed to readily accommodate a range of numerical methods including continuous finite element, finite volume, and discontinuous Galerkin methods. FIERRO is designed to support explicit and implicit time integration methods. FIERRO only supports a single material in an element. No physical data exists within the code.

Morgan, Nathaniel↗

DOE OSTI2013

The MCDB System for Management and Analysis of Petabyte-Scale Uncertain Data

Analysts working with very large data sets often use statistical models to “guess” at unknown, inaccurate, or missing information associated with the data. For example, a distant object viewed through an optical lens will have its position slightly shifted by imperfections in the lens. Thus, rather than considering the object’s observed position to be absolutely correct, it makes sense to take into account the lens’s imperfections to obtain a probabilistic guess as to the object’s true position. For another example, it might be important to associate some sort of error distribution with each of the individual sensors in an array of magnetometers. This error distribution may be complex and include spatially-driven covariances, because errors in nearby sensors are likely to be correlated (caused, for example, by the presence of some nearby, fixed metal object). This project is concerned with the design and implementation of a prototype data management system called the Monte Carlo Database System, or MCDB for short. MCDB allows an expert-level analyst or statistician to attach arbitrary stochastic models to very large data sets in order to “guess” the values for unknown or inaccurate data, such as the actual position of the observed object in the lens example above. When the resulting data set is analyzed, the underlying stochastic models are used to generate hundreds or thousands of possible data set instances, and each of those possible instances is analyzed separately by MCDB. Thus, MCDB does not just give a single answer to the analysis, but it actually gives an empirical distribution of query results that embody the underlying uncertainty, and can in turn be analyzed using standard statistical techniques. The stochastic models in MCDB are implemented as user-defined, external C++ libraries called Variable Generation functions (VG functions for short). Because the VG function interface is exceedingly general, it allows MCDB to be used in a very wide variety of application domains, in conjunction with virtually any stochastic model. Ultimately, we ended up calling the system that we developed over the course of the project SimSQL, to denote the fact that it allowed for stochastic simulation of data. The software developed during the lifetime of the project is available for download from the SimSQL project website: http://cmj4.web.rice.edu/SimSQL/SimSQL.html.

42 ENGINEERING↗

DOE OSTI2025

Keeping LAMMPS cutting edge

Since its inception 30 years ago, LAMMPS has grown to be a world-class molecular dynamics code and a cornerstone of computational materials science research. This project aimed to keep LAMMPS at the forefront of molecular dynamics simulations by adapting LAMMPS to the latest developments in machine learning technology and hardware. Initially, the project set out to provide a unified implementation of active learning for efficient training data generation in LAMMPS, but the research trajectory pivoted to address more immediate and impactful opportunities. On the hardware side, recent record-breaking molecular dynamics simulations were developed on the Cerebras wafer-scale AI chip, and this project has developed an interface between LAMMPS and the hardware-specific molecular dynamics code to accelerate and simplify development and user adoption. On the software side, PyTorch’s Ahead-of-Time (AOT) compilation features promised increased performance for state-of-the-art equivariant neural network potentials, and this project laid the groundwork for their adoption in LAMMPS, resulting in a nearly 20x acceleration in extreme cases. Combined with a comprehensive benchmark study of LAMMPS across all current exascale systems, this project has reinforced LAMMPS’s role as a versatile, high-performance tool for current and future materials science applications.

36 MATERIALS SCIENCE↗

DOE OSTI2025

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Advanced Electron Microscopy of Nanophased Synthetic Polymers and Soft Complexes for Energy and Medicine Applications

After decades of developments, electron microscopy has become a powerful and irreplaceable tool in understanding the ionic, electrical, mechanical, chemical, and other functional performances of next-generation polymers and soft complexes. The recent progress in electron microscopy of nanostructured polymers and soft assemblies is important for applications in many different fields, including, but not limited to, mesoporous and nanoporous materials, absorbents, membranes, solid electrolytes, battery electrodes, ion- and electron-transporting materials, organic semiconductors, soft robotics, optoelectronic devices, biomass, soft magnetic materials, and pharmaceutical drug design. For synthetic polymers and soft complexes, there are four main characteristics that differentiate them from their inorganic or biomacromolecular counterparts in electron microscopy studies: (1) lower contrast, (2) abundance of light elements, (3) polydispersity or nanomorphological variations, and (4) large changes induced by electron beams. Since 2011, the Center for Nanophase Materials Sciences (CNMS) at Oak Ridge National Laboratory has been working with numerous facility users on nanostructured polymer composites, block copolymers, polymer brushes, conjugated molecules, organic–inorganic hybrid nanomaterials, organic–inorganic interfaces, organic crystals, and other soft complexes. This review crystalizes some of the essential challenges, successes, failures, and techniques during the process in the past ten years. It also presents some outlooks and future expectations on the basis of these works at the intersection of electron microscopy, soft matter, and artificial intelligence. Machine learning is expected to automate and facilitate image processing and information extraction of polymer and soft hybrid nanostructures in aspects such as dose-controlled imaging and structure analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Contact Control, Version 1

von Sternberg, Alex↗

DOE OSTI2019

Adiak

Adiak is a computer science data management interface tool for collecting metadata about an application's runs and disseminating it to tools that subscribe to this data. Examples of this metadata could be what user is running an application, what systems it runs on, or application provided name/value pairs. Adiak's capabilities include automated reading of system-level metadata, and a generic type system for applications to register their own name/value metadata. Adiak is currently designed to provide a standard interface that can be integrated with MPI-based applications that run on high performance computing systems. Example tools that use Adiak metadata include performance analysis tools and workflow tools. By allowing the application to specify metadata to Adiak, which then disseminates it to tools, application developers do not have to write to tool-specific interfaces.

LeGendre, MatthewP↗

DOE OSTI2019

Simulation of Spent Nuclear Fuel loading into a Final Waste Repository

Previous work towards studying repository loading have used: - spent nuclear fuel (SNF) with an average burnup composition; - a lumped capacitance thermal model for calculating temperature in a Cyclus repository model. The goal of this work is to improve on the repository models and use U.S. historical SNF inventory data in simulations to more accurately study the loading of a waste repository. These goals will be achieved by: - using UNF-ST-and-DARDS Unified Database (UDB) that has historic assembly-specific data (e.g, isotopic composition, heat) in Cyclus simulations; - implementing a more accurate thermal model within a Cyclus repository model. Objectives: - Create a Cyclus spent fuel conditioning model that packages spent fuel bundles into packages which have user-defined properties. - Create a Cyclus medium-fidelity repository model that gives accurate time and spatial dependent temperature values and loads the repository based on a user-selected loading strategy. Cyclus is an agent-based extensible framework for modeling flow of material through user-defined nuclear fuel cycles. In Cyclus, each facility in the fuel cycle is modeled individually and the facilities interact with one another as independent agents. The spent fuel conditioning model accepts spent fuel bundles and puts them into a cylindrical waste package. In the spent fuel conditioning model, the user can define variables: For each layer, radius, thermal conductivity, thermal diffusivity; For each package, Number of spent fuel bundles, Radius and height. The waste repository model accepts waste packages and emplaces them into available positions within the waste repository based on a thermal criteria. The thermal criteria is a temperature limit at the interface between the waste package surface and the host geology, that is set based on the repository's host geology. In the waste repository model, the user can define the variables: Capacity, Distance between waste packages, Distance between drifts, Repository host geology, Loading Strategy. After the addition of new waste packages at each time step, the waste repository model recalculates the temperature at each location in the repository. If the addition of this new package causes its temperature to exceed the thermal limit, it will be placed back into the buffer. A thermal model that relies on a transient 'outside' model and quasi-steady-state 'inside' model is used to accurately determine the temperature in the repository. The 'outside' model assumes a homogenous medium with the Engineered Barrier System (EBS) replaced by the geologic medium. Temperature solutions for the central waste package, adjacent point and line sources are superimposed to calculate the temperature at specific points in the repository. The central drift consists of one finite line source which represents the central waste package. The central drift also consists of point sources that represent neighboring waste packages in the central drift. The neighboring drifts are represented by infinite line sources. The 'inside' model is considered to be at a quasi-steady-state condition because EBS has a relatively low thermal mass compared to the infinite geologic medium. The steady state calculation is performed at each time step with the heat source and interface temperature as boundary conditions. Future Work: Run Cyclus simulations with U.S. historical SNF inventory data, the spent fuel conditioning and repository models to study how waste package acceptance strategies impact repository loading.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

IDAES-PSE Software Tools for Optimizing Energy Systems and Market Interactions

Modern power grids coordinate electricity production and consumption via multi-scale wholesale energy markets. Historically, levelized cost metrics were the de facto standard for techno-eco-nomic analyses of energy systems and comparison of technology options. However, these metrics neglect the complexity of energy infrastructure including the time-varying value of electricity. An emerging alternative is multi-period optimization, which considers the locational marginal price of electricity as input data (parameters). In this work, we present a general interface for multi-period optimization with time-varying energy prices to facilitate rapid analysis and comparison of potential energy systems models. The PriceTakerModel class is written in the IDAES-PSE platform and allows users to generate a multi-period, price-taker model instance, as well as automatically generate common operational constraints for their model, such as start-up and shutdown. We show this interface successfully generates multi-period price-taker models, facilitates model discrimination, and aids in analyzing various technologies for deployment in unique energy markets.

Laky, Daniel↗

DOE OSTI2018

Toward Transparent Data Management in Multi-layer Storage Hierarchy for HPC Systems

Upcoming exascale high performance computing (HPC) systems are expected to comprise multi-tier storage hierarchy, and thus will necessitate innovative storage and I/O mechanisms. Traditional disk and block-based interfaces and file systems face severe challenges in utilizing capabilities of storage hierarchies due to the lack of hierarchy support and semantic interfaces. Object-based and semantically-rich data abstractions for scientific data management on large scale systems offer a sustainable solution to these challenges. Such data abstractions can also simplify users involvement in data movement. Here, we take the first steps of realizing such an object abstraction and explore storage mechanisms for these objects to enhance I/O performance, especially for scientific applications. We explore how an object-based interface can facilitate next generation scalable computing systems by presenting the mapping of data I/O from two real world HPC scientific use cases: a plasma physics simulation code (VPIC) and a cosmology simulation code (HACC). Our storage model stores data objects in different physical organizations to support data movement across layers of memory/storage hierarchy. Our implementation sclaes well to 16K parallel processes, and compared to the state of the art, such as MPI-IO and HDF5, our object-based data abstractions and data placement strategy in multi-level storage hierarchy achieves up to 7 X I/O performance improvement for scientific data.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Mid Atlantic CHP Technical Assistance Partnership (Final Technical Report)

The Mid Atlantic CHP Technical Assistance Partnership (MACHPTAP), managed by The Pennsylvania State University College of Engineering, served the six states in the Mid-Atlantic region (Pennsylvania, New Jersey, Delaware, Maryland, Virginia and West Virginia) plus the District of Columbia. The objective of the Combined Heat and Power Technical Assistance Partnerships (CHP TAPs) was to provide essential support to continue the market development of CHP’s suite of technologies to further the installation of highly efficient and cost effective CHP. The MACHPTAP’s work included education and outreach as well as technical assistance to a variety of stakeholders including end-users (commercial, industrial, institutional and more), state decision makers, electric and gas utilities, trade associations and non-profit organizations. This assistance included evaluating the economic, energy, reliability and environmental value of proposed systems. The CHP TAPs represented multi-state regions and are the CHP experts in the region who provide fact-based, un-biased information on CHP, including technologies, project development, project financing, local electric and natural gas utility interfaces, and related State best practice policies. Specifically, the MACHPTAP objectives were accomplished through taskings in four specific areas: Technical Assistance to end Users which involved engaging potential end-users to identify, evaluate, and technically support prospective CHP projects; Engagement and Education of End Users where the MACHPTAP engaged and educated end users about CHP, its benefits, and DOE resources available, and strategically hosted or participated in webinars, workshops and conferences; Policymaker Education where the MACHPTAP hosted or participated in webinars, one-on-one meetings, workshops, and other forums; and Program Administration, Management and Reporting, which included monthly and quarterly reporting, program meetings and coordination of activities with other regional TAPs. Accomplishments in the four specific project areas included providing direct Technical Assistance to 289 prospective CHP end users, conducting or participating in 82 End User Education events and hosting or participating in 73 Policy Maker Education events. During the contract period, 107 CHP installations were commissioned in the Mid Atlantic region, with a total generation capacity of over 160 megawatts, with an additional 34 sites with a capacity of over 100 megawatts currently in the planning/design/construction phase. Programmatically, all monthly metrics reports and quarterly reports were submitted in a timely manner.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2024

cclib 2.0: An updated architecture for interoperable computational chemistry

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots—the formalization of cclib’s intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Bayesian Attack Model (BAM) User Story

This document presents a user story for the Bayesian Attack Model (BAM) tool designed to aggregate and analyze cyber-attack observables for operational technology (OT) systems. BAM aims to empower cybersecurity analysts by providing a streamlined interface for collecting observable data from various sources, enabling real-time analysis of potential adversary activity. By enhancing the response capabilities of security teams, BAM facilitates risk-informed decision-making and improves organizational security posture. This user story outlines the key functionalities, user interactions, and requirements necessary to successfully integrate BAM with other security information and event management (SIEM) technology and cybersecurity operations centers (CSOCs).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

The HITRAN2016 molecular spectroscopic database

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is comprised of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 200 additional significant molecules have been added to the database.

Gordon, I. E.↗