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DOE OSTI2018

Toward Automated Tools for Characterization of Molecular Porosity

The emerging advanced porous materials, e.g. extended framework materials and porous molecular materials, offer an unprecedented level of control of their structure and function. The enormous possibilities for tuning these materials by changing their building blocks mean that, in principle, optimally performing materials for a variety of applications can be systematically designed. However, the process of finding a set of optimal structures for a given application requires computational high-throughput tools to analyze and sieve through many candidate materials. In particular, in the case of porous molecular materials, the analysis and selection of a molecule is one of the key aspects as the structure of the molecule determines the structure of the resulting material, and very often the porosity of the molecule significantly contributes to the porous properties of the resulting material. In this work, we introduce definitions and algorithms to characterize porosity at the molecular level, along with a software implementation of these algorithms. We demonstrate applications of the software tool in the discovery and characterization of porous molecules among ca. 94 million molecules currently enlisted in the PubChem database.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Light Water Reactor Sustainability Program: Upgrade of EMRALD to a Modern JavaScript-based Framework

Event Modeling Risk Assessment using Linked Diagrams (EMRALD) is a software tool developed at Idaho National Laboratory for researching the capabilities of dynamic probabilistic risk assessment. It provides a simple interface to represent complex interactions often seen when developing dynamic models. EMRALD can also interface with other applications by modifying inputs, running, and using their results within EMRALD for dynamic and integrated assessment. This report goes over the work performed as part of the Risk-Informed Systems Analysis Pathway under the Light Water Reactor Sustainability program to upgrade the EMRALD software.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

DINGO: Digital assistant to grid operators for resilience management of power distribution system

With increasing adverse weather events and disasters, enabling resiliency of the power distribution system (PDS) is becoming increasingly important. Here in this work, resiliency is defined as the systems ability to keep supplying critical loads even with multiple contingencies. Resiliency may depend on: (a) advanced tools to assist operators in situational awareness and decision making with the increasing volume of data generated by the PDS, (b) visualization and ease of interaction with system resources and information, especially during extreme events and resulting human operator stress, and (c) flexible resources and autonomous control. Operators and support engineers need to interact with the system for key information and take action under stress, given the requirement for decisions in a short time. Integrated technological solutions are prevailing steps to support the most appropriate decision during critical times to serve essential loads. In order to meet the required goals, a Real-time Resiliency Monitoring and Operational Decision Support (RT-RMOD) tool have been developed. It supports various functionalities, including real-time monitoring, resilience assessment, and proactive decision support. However, this work makes advanced feature additions to the tool by developing data-enabled resilience management algorithms for (i) outage detection and localization, (ii) Resiliency-metric driven restoration and reconfiguration, and (iii) NLP based digital assistant for operators called DINGO (DIgital assistaNt to Grid Operators) to interact with Advanced Distribution Management System (ADMS) and RT-RMOD. The developed algorithm was validated for multiple cases of weather events using a real-world, off-grid microgrid system modeled in a real-time simulator, sensor data, and software tools.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2016

Scalable Analysis Methods and In Situ Infrastructure for Extreme Scale Knowledge Discovery

The primary challenge motivating this team’s work is the widening gap between the ability to compute information and to store it for subsequent analysis. This gap adversely impacts science code teams, who are able to perform analysis only on a small fraction of the data they compute, resulting in the very real likelihood of lost or missed science, when results are computed but not analyzed. Our approach is to perform as much analysis or visualization processing on data while it is still resident in memory, an approach that is known as in situ processing. The idea in situ processing was not new at the time of the start of this effort in 2014, but efforts in that space were largely ad hoc, and there was no concerted effort within the research community that aimed to foster production-quality software tools suitable for use by DOE science projects. In large, our objective was produce and enable use of production-quality in situ methods and infrastructure, at scale, on DOE HPC facilities, though we expected to have impact beyond DOE due to the widespread nature of the challenges, which affect virtually all large-scale computational science efforts. To achieve that objective, we assembled a unique team of researchers consisting of representatives from DOE national laboratories, academia, and industry, and engaged in software technology R&D, as well as engaged in close partnerships with DOE science code teams, to produce software technologies that were shown to run effectively at scale on DOE HPC platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Tusqh

SAND2025-00675O Tusqh is a software tool that generates cubical meshes in 2D and 3D and computes the homology of these meshes using persistent homology. It includes a grid cell in the output if its volume-fraction is above a selectable threshold, estimated by sampling points within the cell. Tusqh incorporates anti-aliasing algorithms to mitigate grid orientation and scale effects. It is designed for creating finite element meshes for simulations and can be used in various applications such as heat diffusion, mechanical simulations, and computer graphics rendering. The software outputs meshes in an open format compatible with downstream software. 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.

SciDAC↗

DOE OSTI2018

CTF_

CTF is a thermal-hydraulic simulation tool designed for modeling the reactor vessel region of light water reactors. The code is capable of modeling both coolant and solid regions and includes a nuclear fuel rod model. Coolant is represented with a 9-equation (two phases plus droplets and non-condensable gas) model with closure relationships being provided for normal and accident conditions. Meshing is done using the subchannel approach, which models the coolant region as a collection of parallel 1-D flow paths that communicate laterally through "gaps". CTF also includes a collection of supporting software tools that include: Xml2ctf - A utility for creating native CTF input decks from a simplified input file; pyCTF - A collection of Python utilities used for post-processing CTF results, manipulating CTF input models, and testing differences between output files; CTFFuel - A separate front-end to the CTF fuel rod solver package; Multistate - A separate driver for CTF that communicates through the code coupling interface; and veraAPI - A c++ interface to the code.

Salko, Robert K↗

DOE OSTI2015

Wireless infrastructure protection using low-cost radio frequency fingerprinting receivers

We report that low-data-rate wireless networks incorporated in critical infrastructure applications can be protected through 128-bit encryption keys and address-based access control lists. However, these bit-level credentials are vulnerable to interception, extraction and spoofing using software tools available free of charge on the Internet. Recent research has demonstrated that wireless physical layer device fingerprinting can be used to defend against replay and spoofing attacks. However, radio frequency (RF) fingerprinting typically uses expensive signal collection systems; this is because fingerprinting wireless devices with low-cost receivers has been reported to have inconsistent accuracy. In conclusion, this paper demonstrates a robust radio frequency fingerprinting process that is consistently accurate with both high-end and low-cost receivers. Indeed, the results demonstrate that low-cost software-defined radios can be used to perform accurate radio frequency fingerprinting and to identify spoofing attacks in critical IEEE 802.154-based infrastructure networks such as ZigBee.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Ultra-low-dose limited renal CT for volumetric stone surveillance: advantages over standard unenhanced CT

Purpose: To describe and validate a novel CT approach using volumetric analysis for renal stone surveillance. Materials and methods: This prospective trial consisted of a standard low-dose non-contrast CT (SLD) of the abdomen and pelvis, immediately followed by an ultra-low-dose non-contrast CT (ULD) with reconstruction limited to the kidneys. A novel dedicated software tool was applied that automates stone volume, density, and maximum linear size. Manual linear stone size was measured by a radiology fellow and urology resident for comparison. CT dose and clinical charges were considered. Results: Twenty-eight stones in 16 patients were analyzed. Mean effective dose of ULD CT was 0.57 mSv, an average 92% lower than the SLD CT dose. For SLD, mean size ± SD (range) (mm) was 7.9 ± 6.2 (2.6–30.5) for Reader 1, 7.3 ± 6 (2.4–30.7) for Reader 2, and 9.3 ± 6.4 (3.7–33.1) for the automated software. For ULD, mean size ± SD (range) (mm) was 7.3 ± 6 (2.5–30.5) for Reader 1, 7.2 ± 6.1 (2.1–30.7) for Reader 2, and 9.1 ± 6.4 (4.2–32.8) for the automated software. Automated stone diameters were larger than manual diameters for 27/28 stones (mean difference, 23%); difference was ≥ 2 mm in 30%. Average variability between manual measurements was 8.6% (SLD) and 7.8% (ULD), but was 0% for the automated technique. Our institutional charge for ULD renal CT is slightly less than renal US, and > 4× less than SLD CT. The Medicare global fee for the ULD renal CT is less than the SLD CT of the abdomen and pelvis. Conclusions: This focused stone surveillance CT protocol is lower cost and lower dose compared to the standard CT approach. Automated assessment of stone burden provides improved reproducibility over manual linear measurement and offers the advantages of 3D measurements and volumetry. We now offer and perform this protocol in routine clinical practice for stone surveillance.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2015

Monitoring Wildlife Interactions with Their Environment: An Interdisciplinary Approach

In a rapidly changing world, wildlife ecologists strive to correctly model and predict complex relationships between animals and their environment, which facilitates management decisions impacting public policy to conserve and protect delicate ecosystems. Recent advances in monitoring systems span scientific domains, including animal and weather monitoring devices and landscape classification mapping techniques. The current challenge is how to combine and use detailed output from various sources to address questions spanning multiple disciplines. WolfScout wildlife and weather tracking system is a software tool capable of filling this niche. WolfScout automates integration of the latest technological advances in wildlife GPS collars, weather stations, drought conditions, and severe weather reports, and animal demographic information. The WolfScout database stores a variety of classified landscape maps including natural and manmade features. Additionally, WolfScout’s spatial database management system allows users to calculate distances between animals’ location and landscape characteristics, which are linked to the best approximation of environmental conditions at the animal’s location during the interaction. Through a secure website, data are exported in formats compatible with multiple software programs including R and ArcGIS. The WolfScout design promotes interoperability in data, between researchers, and software applications while standardizing analyses of animal interactions with their environment.

Spatial database management system, Wildlife, Weat↗

DOE OSTI2015

Final Report to the National Energy Technology Laboratory on FY09-FY13 Cooperative Research with the Consortium for Electric Reliability Technology Solutions

The Consortium for Electric Reliability Technology Solutions (CERTS) was formed in 1999 in response to a call from U.S. Congress to restart a federal transmission reliability R&D program to address concerns about the reliability of the U.S. electric power grid. CERTS is a partnership between industry, universities, national laboratories, and government agencies. It researches, develops, and disseminates new methods, tools, and technologies to protect and enhance the reliability of the U.S. electric power system and the efficiency of competitive electricity markets. It is funded by the U.S. Department of Energy’s Office of Electricity Delivery and Energy Reliability (OE). This report provides an overview of PSERC and CERTS, of the overall objectives and scope of the research, a summary of the major research accomplishments, highlights of the work done under the various elements of the NETL cooperative agreement, and brief reports written by the PSERC researchers on their accomplishments, including research results, publications, and software tools.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2017

Water Quality Projects Summary for the Mid-Columbia and Cumberland River Systems

Scheduling and operational control of hydropower systems is accompanied with a keen awareness of the management of water use, environmental effects, and policy, especially within the context of strict water rights policy and generation maximization. This is a multi-objective problem for many hydropower systems, including the Cumberland and Mid-Columbia river systems. Though each of these two systems have distinct operational philosophies, hydrologic characteristics, and system dynamics, they both share a responsibility to effectively manage hydropower and the environment, which requires state-of-the art improvements in the approaches and applications for water quality modeling. The Department of Energy and Oak Ridge National Laboratory have developed tools for total dissolved gas (TDG) prediction on the Mid-Columbia River and a decision-support system used for hydropower generation and environmental optimization on the Cumberland River. In conjunction with IIHR - Hydroscience & Engineering, The University of Iowa and University of Colorado s Center for Advanced Decision Support for Water and Environmental Systems (CADSWES), ORNL has managed the development of a TDG predictive methodology at seven dams along the Mid-Columbia River and has enabled the ability to utilize this methodology for optimization of operations at these projects with the commercially available software package Riverware. ORNL has also managed the collaboration with Vanderbilt University and Lipscomb University to develop a state-of-the art method for reducing high-fidelity water quality modeling results into surrogate models which can be used effectively within the context of optimization efforts to maximize generation for a reservoir system based on environmental and policy constraints. The novel contribution of these efforts is the ability to predict water quality conditions with simplified methodologies at the same level of accuracy as more complex and resource intensive computing methods. These efforts were designed to incorporate well into existing hydropower and reservoir system scheduling models, with runtimes that are comparable to existing software tools. In addition, the transferability of these tools to assess other systems is enhanced due the use of simplistic and easily attainable values for inputs, straight-forward calibration of predictive equation coefficients, and standardized comparison of traditionally familiar outputs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Generative Models for Crystalline Materials

Understanding structure-property relationships in materials is fundamental in condensed matter physics and materials science. Over the past few years, machine learning (ML) has emerged as a powerful tool for advancing this understanding and accelerating materials discovery. Early ML approaches primarily focused on constructing and screening large material spaces to identify promising candidates for various applications. More recently, research efforts have increasingly shifted toward generating crystal structures using end-to-end generative models. This review analyzes the current state of generative modeling for crystal structure prediction and de novo generation. It examines crystal representations, outlines the generative models used to design crystal structures, and evaluates their respective strengths and limitations. Furthermore, the review highlights experimental considerations for evaluating generated structures and provides recommendations for suitable existing software tools. Emerging topics, such as modeling disorder and defects, integration in advanced characterization, incorporating synthetic feasibility constraints, and model explainability are explored. Ultimately, this work aims to inform both experimental scientists looking to adapt suitable ML models to their specific circumstances and ML specialists seeking to understand the unique challenges related to inverse materials design and discovery.

Metni, Houssam [Karlsruhe Inst. of Technology (KIT↗

DOE OSTI2016

Arion

Arion is a library and tool set that enables researchers to holistically define test system models. To define a complex system for testing an algorithm or control requires expertise across multiple domains. Simulating a complex system requires the integration of multiple simulators and test hardware, each with their own specification languages and concepts. This requires extensive set of knowledge and capabilities. Arion was developed to alleviate this challenge. Arion is a library of Java libraries that abstracts the concepts from supported simulators into a cohesive model language that allows someone to build models to their needed level of fidelity and expertise. Arion is also a software tool that translates the users model back into the specification languages of the simulators and test hardware needed for execution.

Fisher, Andy↗

DOE OSTI2016

Arion

Source record↗

DOE OSTI2017

Automated Proton Track Identification in MicroBooNE Using Gradient Boosted Decision Trees

MicroBooNE is a liquid argon time projection chamber (LArTPC) neutrino experiment that is currently running in the Booster Neutrino Beam at Fermilab. LArTPC technology allows for high-resolution, three-dimensional representations of neutrino interactions. A wide variety of software tools for automated reconstruction and selection of particle tracks in LArTPCs are actively being developed. Short, isolated proton tracks, the signal for low- momentum-transfer neutral current (NC) elastic events, are easily hidden in a large cosmic background. Detecting these low-energy tracks will allow us to probe interesting regions of the proton's spin structure. An effective method for selecting NC elastic events is to combine a highly efficient track reconstruction algorithm to find all candidate tracks with highly accurate particle identification using a machine learning algorithm. We present our work on particle track classification using gradient tree boosting software (XGBoost) and the performance on simulated neutrino data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2015

A Process for Modelling Diffuse Scattering from Disordered Molecular Crystals, Illustrated by Application to Monoclinic 9-Chloro-10-methylanthracene

Diffuse scattering from a crystal contains valuable information about the two-body correlations (related to the nanoscale order) in the material. Despite years of development, the detailed analysis of single crystal diffuse scattering (SCDS) has yet to become part of the everyday toolbox of the structural scientist. Recent decades have seen the pair distribution function approach to diffuse scattering (in fact, total scattering) from powders become a relatively routine tool. However, analysing the detailed, complex, and often highly anisotropic three-dimensional distribution of SCDS remains valuable yet rare because there is no routine method for undertaking the analysis. At present, analysis requires significant investment of time to develop specialist expertise, which means that the analysis of diffuse scattering, which has much to offer, is not incorporated thorough studies of many compounds even though it has the potential to be a very useful adjunct to existing techniques. This article endeavours to outline in some detail how the diffuse scattering from a molecular crystal can be modelled relatively quickly and largely using existing software tools. It is hoped this will provide a template for other studies. To enable this, the entire simulation is included as deposited material.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Unified Nanotechnology Format: One Way to Store Them All

The domains of DNA and RNA nanotechnology are steadily gaining in popularity while proving their value with various successful results, including biosensing robots and drug delivery cages. Nowadays, the nanotechnology design pipeline usually relies on computer-based design (CAD) approaches to design and simulate the desired structure before the wet lab assembly. To aid with these tasks, various software tools exist and are often used in conjunction. However, their interoperability is hindered by a lack of a common file format that is fully descriptive of the many design paradigms. Therefore, in this paper, we propose a Unified Nanotechnology Format (UNF) designed specifically for the biomimetic nanotechnology field. UNF allows storage of both design and simulation data in a single file, including free-form and lattice-based DNA structures. By defining a logical and versatile format, we hope it will become a widely accepted and used file format for the nucleic acid nanotechnology community, facilitating the future work of researchers and software developers. Together with the format description and publicly available documentation, we provide a set of converters from existing file formats to simplify the transition. Finally, we present several use cases visualizing example structures stored in UNF, showcasing the various types of data UNF can handle.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2020

Bayes Inference Engine (BIE) Test Plan: TiltConeBeamComboDMLinear

The Bayes Inference Engine (BIE) is a general software tool intended to be used primarily in the analysis of radiographic data for density. An analysis is set up in the BIE by representing the problem as a collection of modules called glyphs. All glyphs to be used in creating the forward model of the experiment will be tested separately for a range of inputs.

97 MATHEMATICS AND COMPUTING↗