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DOE OSTI2022

A mass–momentum consistent coupling for mesh-adaptive two-phase flow simulations

Here, we present a novel mass-momentum consistent coupling between a geometric volume-of-fluid scheme and an incompressible flow solver with differing directional-splitting approaches. The advection of the volume fraction is performed using a direction-split algorithm, whereas the momentum advection algorithm uses a traditional unsplit, fractional-step approach. Both algorithms employ finite-volume discretizations based on Cartesian meshes. In solving the mass-momentum consistency problem, momentum fluxes at the cell faces are weighted by the density fluxes based on the already advected volume fraction. The success of our approach lies on introducing a Favre-averaged velocity interpolation at the liquid/gas interface along with a minmod slope limiter. Mesh-convergence studies show that when the minmod slope limiter is used, the two-phase solver retains an accuracy between first and second order, but when a purely upwind scheme is considered, its accuracy drops to first order. Finally, after considering several validation problems, the solver is shown to agree well with reference numerical and experimental data while retaining its robustness and efficiency.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Stress field analysis in a stony meteorite under thermal fatigue and mechanical loadings

A micromechanical approach relying on 3D image-based finite element (FE) models, together with experimental testing, is employed to investigate the stress distribution in an L6 ordinary chondrite's microstructure subjected to thermal and mechanical loadings. An in-situ X-ray micro-computed tomography (micro-CT) setup capable of applying thermal and mechanical loads shed light on crack initiation mechanisms in chondrite samples. Micro-CT images were further used to reconstruct realistic microstructural models of the samples, which were transformed into FE models using an automated non-iterative mesh generation algorithm. FE approximation of stress fields showed that under mechanical loads, the stress often concentrates in matrix-particle interfacial regions with higher curvatures. Furthermore, this could result in the nucleation and eventually propagation of cracks in such regions. However, when the thermal cycling takes place, the stress concentrates more uniformly along with particle interfaces, resulting in their debonding from the surrounding matrix. Both observations were verified by experimental data obtained from in-situ micro-CT imaging.

36 MATERIALS SCIENCE↗

DOE OSTI2020

PERSIANN Dynamic Infrared–Rain Rate (PDIR-Now): A Near-Real-Time, Quasi-Global Satellite Precipitation Dataset

This study presents the Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks–Dynamic Infrared Rain Rate (PDIR-Now) near-real-time precipitation dataset. This dataset provides hourly, quasi-global, infrared-based precipitation estimates at 0.04° × 0.04° spatial resolution with a short latency (15–60 min). It is intended to supersede the PERSIANN–Cloud Classification System (PERSIANN-CCS) dataset previously produced as the near-real-time product of the PERSIANN family. We first provide a brief description of the algorithm’s fundamentals and the input data used for deriving precipitation estimates. Second, we provide an extensive evaluation of the PDIR-Now dataset over annual, monthly, daily, and subdaily scales. Last, the article presents information on the dissemination of the dataset through the Center for Hydrometeorology and Remote Sensing (CHRS) web-based interfaces. The evaluation, conducted over the period 2017–18, demonstrates the utility of PDIR-Now and its improvement over PERSIANN-CCS at all temporal scales. Specifically, PDIR-Now improves the estimation of rain/no-rain days as demonstrated by a critical success index (CSI) of 0.53 compared to 0.47 of PERSIANN-CCS. In addition, PDIR-Now improves the estimation of seasonal and diurnal cycles of precipitation as well as regional precipitation patterns erroneously estimated by PERSIANN-CCS. Finally, an evaluation is carried out to examine the performance of PDIR-Now in capturing two extreme events, Hurricane Harvey and a cluster of summer thunderstorms that occurred over the Netherlands, where it is shown that PDIR-Now adequately represents spatial precipitation patterns as well as subdaily precipitation rates with a correlation coefficient (CORR) of 0.64 for Hurricane Harvey and 0.76 for the Netherlands thunderstorms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Particle Tracking Methods for Battery Precipitation Reactions

Precipitation and deposition reactions at solid–liquid interfaces play a key role in a number of battery chemistries, including Li-ion, so-called “anode free” batteries, zinc-based battery chemistries, and lithium–sulfur, among others. Although models with heterogeneous nucleation and growth phenomena are present in the literature, papers have not to date provided much detail on the numerical algorithms used to track the temporal evolution of the particle size distribution of deposits on electrode surfaces. In this paper we examine several approaches to discretize and track the particle size distribution, demonstrating that common approaches lead to anomalous flattening of the particle size distribution. We conclude by presenting an algorithm that preserves the appropriate particle size distribution during particle growth.

Algorithms↗

DOE OSTI2021

Status Report on the INL IES Plug-and-Play Framework

This report discusses the advancements and status of the flexible plug-and-play framework development currently ongoing that aims to integrate Modelica/Dymola with the Risk Analysis and Virtual ENvironment (RAVEN) software in terms of both Functional Mock-Up Interface (FMI)/Functional Mock-Up Unit (FMU) construction and usage, which aims to ease the sharing and simulation of complex dynamic models. This report discusses the FMI/FMU development advancements, overall focusing on the deployment of methodologies for RAVEN to export and use FMI/FMU of both Python-based models and advanced AI-constructed algorithms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Hydro-chemo-mechanical phase field formulation for corrosion induced cracking in reinforced concrete

Steel corrosion induced cracking in reinforced concrete structures is often caused by volumetric straining at the steel-concrete interface. This volumetric strain is mainly controlled by the rate of generation of corrosion product, which depends on the diffusion of Cl{sup −} and dissolved O{sub 2} as well as the chemical reaction at the steel-concrete interface. While many numerical modeling techniques have been proposed to tackle this complex phenomenon, most have been limited to using staggered solution schemes, where the diffusion, chemical reaction, mechanical strain, and crack fields are solved for separately. Unfortunately, such approaches introduce numerical errors that can lead to unrealistic predictions. Therefore, a coupled solution, is needed to remove the formulation induced errors and understand this complex phenomenon. To provide a unifying solution framework for corrosion induced cracking in reinforced concrete, a phase field formulation is presented and implemented with FEM algorithms. The governing equations are derived from the system's free energy and Fick's law of diffusion. The proposed formulation was first validated in 1D by comparing the modeling results with the semi-analytical solution approximated via Laurent series to avoid singularities in the complex domain. 2D plane strain solutions to the embedded rebar undergoing corrosion induced cracking with pre-cracks are also presented and compared with the approximated solutions from linear elastic fracture mechanics theory (LEFM). The modeling of crack propagation enabled by the proposed formulation is also presented along with parametric studies to reveal the roles of the fracture toughness and permeability of the concrete on the corrosion induced cracking. A case study was also conducted on H-pile steel with concrete jackets to demonstrate the feasibility of modeling corrosion induced fracture in reinforced concrete structures with complex steel-concrete interfaces.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Discussion on molecular dynamics (MD) simulations of the asphalt materials

The application of asphalt materials in pavement engineering has been increasingly widespread and sophisticated over the past several decades. Variations in the properties of asphalt binder during mixing, transportation, and paving can affect the performance of asphalt pavement. However, the asphalt material is a non-homogeneous and complex organic substance, consisting of various molecules with widely various molecular weights, elemental compositions, and structures. This complexity leads to difficulties for researchers to clearly and immediately understand the properties of asphalt materials and their variations. The multi-scale research approach combines macroscopic experimental data and microscopic simulation results from a practical engineering perspective. It helps to improve the understanding of asphalt materials. The molecular dynamics (MD) simulation proposes a corresponding molecular model of asphalt material based on experimental data, and the simulation algorithm is able to derive properties similar to those of real asphalt. Here, this paper provides a comprehensive review of the current studies on MD simulation of asphalt materials, including modeling, properties, and multi-scale analysis. As a key part of the computational simulation, this paper discusses the typical asphalt binder and asphalt-aggregate interface models constructed by different groups, and also presents their differences from real samples and their feasibility based on fundamental properties. After the introduction of molecular models, the extensive work made by researchers based on molecular models is categorically reviewed and discussed. The strengths and weaknesses of MD simulation methods in the study of asphalt materials are also summarized in order to provide the reader with a more comprehensive understanding of the relevant contents and to guide subsequent research.

36 MATERIALS SCIENCE↗

DOE OSTI2026

A robust framework for frictional fault contact in geological formations using a stabilized augmented Lagrangian approach

Numerical simulations are essential to evaluate the performance and safety of engineered subsurface systems such as geological carbon storage sites, enhanced geothermal fields, and oil and gas reservoirs. A key challenge lies in accurately modeling the frictional contact behavior along fault surfaces. This problem involves inequality constraints that arise from the physics of frictional slip, requiring specialized numerical methods to handle the resulting highly nonlinear and path-dependent behavior. Here, in this work, we address this challenge using an Augmented Lagrangian Method (ALM) implemented via the Uzawa algorithm. The formulation employs mixed finite element spaces, combining low-order piecewise linear displacements within the 3D domain cells with piecewise constant tractions defined on the fault surfaces. Furthermore, to ensure stability and satisfy the inf-sup condition, the discrete displacement space is enriched with face bubble functions on both sides of the contact interfaces. This approach offers several advantages over other stabilization techniques that rely on additional terms, and it integrates naturally in the Uzawa framework.

58 GEOSCIENCES↗

DOE OSTI2023

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Broadband Characterization and Circuit Model Development of Transmission-Scale Transformers

This report describes broadband measurements of transmission-scale transformers typical in the electric power grid. This work was performed as part of the EMP Resilient Grid LDRD project at Sandia National Laboratories to generate circuit models that can be used for high-altitude electromagnetic pulse (HEMP) coupling simulations and response predictions. The objective of the work was to obtain characterization data of substation yard equipment across a frequency range relevant to HEMP. Vector network analyzer measurements up to 100 MHz were performed on two power transformers at ABB-Hitachi and a single ITEC potential transformer. Custom cable breakouts were designed to interface with the transformer terminals and provide ground connections to the chassis at the base of the transformer bushings. The three-phase terminals of the power transformers were measured as a common mode impedance using a parallel resistive splitter, and the single-phase terminals of the potential transformer were measured directly. A vector fitting algorithm was used to empirically fit circuit models to the resulting two-port networks and input impedances of the measured objects. Simplified circuit representations of the input impedances were also generated to assess the degree of precision needed for high-altitude electromagnetic pulse response predictions, which were performed in Sandia's XYCE circuit simulator platform. HEMP coupling simulations using the transformer models showed significant reduction in the voltage peak and broadening in the pulse width seen at the power transformer compared to the traveling wave voltage. This indicated the importance of the load condition when defining the coupled insult in an electric power substation. Simplified circuit models showed a similar voltage at the transformer with a smoothed waveform. The presence of potential transformers in the simulation did not significantly change the simulated voltage at the power transformer. Single-port input impedance models were also developed to define load conditions when transfer characteristics were not necessary.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

The essential character of the neutrino mechanism of core-collapse supernova explosions

Abstract Calibrating with detailed 2D core-collapse supernova (CCSN) simulations, we derive a simple CCSN explosion condition based solely upon the terminal density profiles of state-of-the-art stellar evolution calculations of the progenitor massive stars. This condition captures the vast majority of the behaviour of the one hundred 2D state-of-the-art models we performed to gauge its usefulness. The goal is to predict, without resort to detailed simulation, the explodability of a given massive star. We find that the simple maximum fractional ram pressure jump discriminant we define works well ∼90 per cent of the time and we speculate on the origin of the few false positives and false negatives we witness. The maximum ram pressure jump generally occurs at the time of accretion of the silicon/oxygen interface, but not always. Our results depend upon the fidelity with which the current implementation of our code F ornax adheres to Nature and issues concerning the neutrino–matter interaction, the nuclear equation of state, the possible effects of neutrino oscillations, grid resolution, the possible role of rotation and magnetic fields, and the accuracy of the numerical algorithms employed remain to be resolved. Nevertheless, the explodability condition we obtain is simple to implement, shows promise that it might be further generalized while still employing data from only the unstable Chandrasekhar progenitors, and is a more credible and robust simple explosion predictor than can currently be found in the literature.

Astronomy & Astrophysics↗

DOE OSTI2022

Shallow Cumulus Entrainment Dynamics in a Sheared Environment

Abstract Vertical wind shear has long been known to tilt convective towers and reduce thermal ascent rates. The purpose of this study is to better understand the physical mechanisms responsible for reduced ascent rates in shallow convection. In particular, the study focuses on cloud-edge mass flux to assess how shear impacts mass-flux profiles of both the ensemble and individual clouds of various depths. A compositing algorithm is used to distill large-eddy simulation (LES) output to focus on up- and down-shear cloud edges that are not influenced by complex cloud geometry or nearby clouds. A direct entrainment algorithm is used to estimate the mass flux through the cloud surface. We find that the dynamics on the up- and down-shear sides are fundamentally different, with the entrainment of environmental momentum and dilution of buoyancy being primarily responsible for the reduced down-shear ascent rates. Direct estimates of fluid flow through the cloud interface indicate a counter-shear organized flow pattern that entrains on the down-shear side and detrains on the up-shear side, resulting from the subcloud shear being lifted into the cloud layer by the updraft. In spite of organized regions of entrainment and detrainment, the overall net lateral mass flux remains unchanged with respect to the no shear run, with weak detrainment present throughout cloud depth.

Meteorology & Atmospheric Sciences↗

DOE OSTI2025

Automating Anomaly Detection for Target systems at Spallation Neutron Source

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory, produces the world’s most intense pulse neutrons beams. An accelerated proton beam is directed into a mercury target to generate neutrons via spallation. The target system accounted for over 40% of the overall downtime of the facility in 2022. Thus, early detection in anomalies in the target systems can enable taking corrective actions to avoid failures and reduce downtime. Fault prognostics and anomaly detection in accelerators, both at SNS and outside, has largely focused on the beam side. This paper presents one the first studies exploring leveraging machine learning to automate the detection of anomalies in the target system. The target system consists of over 30 different interconnected subsystems, and the present work focuses on the mercury process system as a use case. Analyzing data from 28 process variables from 2022 and 2023, tree-based and reconstruction-based algorithms are employed to detect anomalies in archived data. The algorithms detected previously unreported anomalies, several of which were deemed alert worthy by human experts, particularly those found by reconstruction-based algorithms. Using data from each production run in the accelerator increased the generalizability of the models in time. Efforts are now underway to implement a workflow for incorporating human feedback to update the models and evaluating performance on unseen data. The models will eventually be integrated into the existing System Tracking and Reliability system with a web interface for automated anomaly detection and reporting along with a pathway for incorporating human feedback for model updates.

Raj, Anant [ORNL] (ORCID:0000000306711244)↗

DOE OSTI2025

sourcePy

Pollutant source identification techniques (of which there are many variations) are either locked behind researchers writing their own code for each use case or GUI platforms that are easy to use but inflexible and opaque. The Python package sourcePy brings together many of the pollutant source identification algorithms, giving the user full control out of the box. It aims to create a platform for source identification experiments where the full analysis from beginning to end can be done in Python, with a level of specificity in design that isn't available in the GUI options. sourcePy provides users with a few key features: -A Python interface with HYSPLIT, which can be used to generate trajectories and concentration plumes -Several Python classes which standardize the preparation and processing of data related to source identification experiments -Example scripts and notebooks that allow even new python users to get started with their own experiments quickly -Visualization methods

Arseneau, Isaac [Oak Ridge National Laboratory (OR↗

DOE OSTI2022

A comprehensive guide to the physics and usage of PYTHIA 8.3

This manual describes the Pythia event generator, the most recent version of an evolving physics tool used to answer fundamental questions in particle physics. The program is most often used to generate high-energy-physics collision “events”, i.e. sets of particles produced in association with the collision of two incoming high-energy particles, but has several uses beyond that. The guiding philosophy is to produce and re-produce properties of experimentally obtained collisions as accurately as possible. The program includes a wide ranges of reactions within and beyond the Standard Model, and extending to heavy ion physics. Emphasis is put on phenomena where strong interactions play a major role. The manual contains both pedagogical and practical components. All included physics models are described in enough detail to allow the user to obtain a cursory overview of used assumptions and approximations, enabling an informed evaluation of the program output. A number of the most central algorithms are described in enough detail that the main results of the program can be reproduced independently, allowing further development of existing models or the addition of new ones. Finally, a chapter dedicated fully to the user is included towards the end, providing pedagogical examples of standard use cases, and a detailed description of a number of external interfaces. The program code, the online manual, and the latest version of this print manual can be found on the Pythia web page: https://www.pythia.org/.

Bierlich, Christian↗

DOE OSTI2022

Codebase release 8.3 for PYTHIA

Bierlich, Christian↗

DOE OSTI2021

Improved Understanding of Coupled Water and Carbon Cycle Processes through Machine Learning Approaches

Focal Area(s): This white paper addresses how explainable machine learning (ML) algorithms can improve insights gained from complex data (Focal Area 3). We will also address how ML approaches related to sensor compression and low energy AI hardware can be used for efficient data acquisition (Focal Area 1). Science Challenge: We will focus on the coupled water cycle and carbon cycle processes in terrestrial ecosystems and terrestrial-aquatic interfaces. Thus, our approaches will be centered around several data-model integration challenges indicated in EESD strategic plans for two science focus areas: Terrestrial Ecosystem Science and Hydrobiogeochemistry. We can use AI to correct systematic model errors due to biases in either data or model structure/processes. Error patterns in model predictions usually vary by region, model, season etc. But there are systematic patterns in them. e.g., soil moisture tends to be overestimated in the arid western continental United States underestimated in wetter eastern USA; some land surface models tend to underestimate moisture in wet seasons and overestimate in dry seasons. Moreover, the consequences of extreme events (e.g., drought, extreme flooding, storm surges associated with tropical storms, hurricanes) on carbon cycle processes are not well represented in ecosystem and Earth system models. Redox-sensitive processes (e.g., rapid oxidation/reduction of iron and other redox-sensitive elements in soil microsites subjected to fluctuated hydrology) in terrestrial-aquatic interfaces further challenge model predictions of hot-spots (and hot-moments) due to poor understanding of underlying mechanisms. Thus, AI/ML approaches can be used to learn patterns in the data and model errors and use them to build model equations and correct process-based model errors.

54 ENVIRONMENTAL SCIENCES↗