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DOE OSTI2021

Development of an integrated core–edge scenario using the super H-mode

An optimized pedestal regime called the super-H (SH) mode is leveraged to couple a fusion relevant core plasma with a high density scrape-off layer appropriate for realistic reactor power exhaust solutions. Recent DIII-D experiments have expanded the operating space of the SH regime using advanced control algorithms and investigated optimization of impurity seeding, deuterium gas puffing, and 3D magnetic perturbations. Simultaneous real-time control of the pedestal density and radiated power with in-vessel coils and nitrogen seeding enable optimal coupled divertor and pedestal conditions. Four case studies are analysed with varied levels of radiated power in the divertor volume ranging from 0 (no seeding) to 8.5 MW radiated from carbon and nitrogen emission. Plasmas with a 4.5 MW radiated power target establish a radiative mantle, leading to divertor temperatures of ~16 eV while maintaining SH-mode, and with only marginal impact on the pedestal and core performance. Increased levels of N 2 seeding with a 7.5 MW radiated power target facilitate detachment onset and divertor temperatures <5 eV, with no degradation in stored energy and the operational point remaining inside the SH-mode channel for $ > 2.5{\tau }_{\text{E}}$. Finally, a 8.5 MW radiated power target leads to partial detachment, which is so far associated with the loss of access to SH-mode pedestal conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Integration of Electromagnetic Geophysics Forward Simulation in Coupled Flow and Geomechanics for Monitoring a Gas Hydrate Deposit Located in the Ulleung Basin, East Sea, Korea

We investigate the feasibility of electromagnetic (EM) geophysics methods to detect the dissociation of gas hydrate specifically from a gas hydrate deposit located in the Ulleung Basin, East Sea, Korea via an integrated flow-geomechanics-EM geophysics simulation. To this end, coupled flow and geomechanics simulation is first performed with the multiple porosity model employed, where a mixed formulation with the finite volume (FV) and finite element (FE) methods are taken for the flow and geomechanics, respectively. From the saturation and porosity fields obtained from the coupled flow and geomechanics, the electrical conductivity model is established for the EM simulation. Solving the partial differential equation of electrical diffusion which is linearized using the 3D finite element method (FEM), the EM fields are then computed. For numerical experiments, particularly two approaches in the configuration for the EM methods are compared in this contribution: the surface-to-surface and the surface-to-borehole methods. When the surface-to-surface EM method is employed, the EM is found to be less sensitive, implying low detectability. Especially for the short term of production, the low detectability is attributed to the similarity of electrical resistivity between the dissociated gas (CH4) and hydrate as well as the specific dissociation pattern within the intercalated composites of the field. On the other hand, when the surface-to-borehole EM method is employed, its sensitivity to capture the produced gas flow is improved, confirming its detectability in monitoring gas flow. Hence, the EM geophysics simulation integrated with coupled flow and geomechanics can be a potential tool for monitoring gas hydrate deposits.

depressurization↗

DOE OSTI2023

Implementation and experimental validation of nonlocal damage in a large-strain elasto-viscoplastic FFT-based framework for predicting ductile fracture in 3D polycrystalline materials

Ductile materials, such as metal alloys, can undergo substantial deformation before failure. Additionally, these materials are usually of polycrystalline composition and exhibit strongly anisotropic behavior at small length scales. Previously developed fast Fourier transform (FFT)-based models can model ductile fracture of isotropic materials or the elastic–plastic behavior of anisotropic polycrystalline materials; however, there remains a need to couple both capabilities. This work extends a large-strain FFT-based crystal plasticity model to simulate ductile fracture of polycrystalline materials. In this work, a triaxiality-based continuum damage mechanics (CDM) formulation is incorporated into a large-strain elasto-viscoplastic FFT (LS-EVPFFT) framework. The CDM formulation is augmented with an integral-based nonlocal regularization approach that correctly handles gas-phase material necessary to model unconstrained surfaces. To validate the damage-enabled LS-EVPFFT framework, mesoscale copper tensile coupons were machined using microwire electrical discharge machining and experimentally characterized using electron backscatter diffraction. In-situ optical digital image correlation was performed during uniaxial testing to provide a side-by-side comparison of the experimental and computational strain fields and stress–strain responses. The damage-enabled LS-EVPFFT framework can simulate the complete macroscopic stress–strain response of ductile polycrystals to failure. The model reproduces necking behavior that qualitatively agrees with experimental observations. By leveraging the relatively low computational cost of the damage-enabled LS-EVPFFT framework, the framework presented here allows the ductile fracture response of 3D polycrystalline materials to be tractably predicted.

36 MATERIALS SCIENCE↗

DOE OSTI2022

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

4D Printing via an Unconventional Fused Deposition Modeling Route to High-Performance Thermosets

An unprecedented four-dimensional (4D) printing process allowing high-performance and shape memory thermoset to be printed, for the first time, by fused deposition modeling (FDM) with isotropic properties has been achieved. Here, bisphenol A-based epoxy and benzoxazine were formulated to a low-temperature thermoplastic and high-temperature thermoset resin, which is melt-extrudable and can be postcured into covalently cross-linked material. Carbon nanotube (CNT) was added in the resin to work as both mechanical enhancement filler and rheology modifier to prevent shape deformation during postcuring process. The cross-layer reaction fuses individual layers into an integrity, thus eliminating layer delamination induced by FDM, offering isotropic mechanical properties regardless of the printing orientations. The highly cross-linked network provides outstanding mechanical strength and superb thermal stability. The excellent shape memory performance with fast recovery rate and large recovery degree is also obtained in the three-dimensional (3D) printed composites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Evaluating the Representations of Atmospheric Rivers and Their Associated Precipitation in Reanalyses With Satellite Observations

Atmospheric rivers (ARs) are filaments of enhanced horizontal moisture transport in the atmosphere. Due to their prominent role in the meridional moisture transport and regional weather extremes, ARs have been studied extensively in recent years. Yet, the representations of ARs and their associated precipitation on a global scale remains largely unknown. In this study, we developed an AR detection algorithm specifically for satellite observations using moisture and the geostrophic winds derived from 3D geopotential height field from the combined retrievals of the Atmospheric Infrared Sounder and the Advanced Microwave Sounding Unit on NASA Aqua satellite. This algorithm enables us to develop the first global AR catalog based solely on satellite observations. The satellite–based AR catalog is then combined with the satellite–based precipitation (Integrated Muti–SatellitE Retrievals for GPM) to evaluate the representations of ARs and AR–induced precipitation in reanalysis products. Here our results show that the spreads in AR frequency and AR length distribution are generally small across data sets, while the spread in AR width is relatively larger. Reanalysis products are found to consistently underestimate both mean and extreme AR–related precipitation. However, all reanalyses tend to precipitate too often under AR conditions, especially over low latitude regions. This finding is consistent with the “drizzling” bias which has plagued generations of climate models. Overall, the findings of this study can help to improve the representations of ARs and associated precipitation in reanalyses and climate models.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

2D-FFTLog: efficient computation of real-space covariance matrices for galaxy clustering and weak lensing

ABSTRACT Accurate covariance matrices for two-point functions are critical for inferring cosmological parameters in likelihood analyses of large-scale structure surveys. Among various approaches to obtaining the covariance, analytic computation is much faster and less noisy than estimation from data or simulations. However, the transform of covariances from Fourier space to real space involves integrals with two Bessel integrals, which are numerically slow and easily affected by numerical uncertainties. Inaccurate covariances may lead to significant errors in the inference of the cosmological parameters. In this paper, we introduce a 2D-FFTLog algorithm for efficient, accurate, and numerically stable computation of non-Gaussian real-space covariances for both 3D and projected statistics. The 2D-FFTLog algorithm is easily extended to perform real-space bin-averaging. We apply the algorithm to the covariances for galaxy clustering and weak lensing for a Dark Energy Survey Year 3-like and a Rubin Observatory’s Legacy Survey of Space and Time Year 1-like survey, and demonstrate that for both surveys, our algorithm can produce numerically stable angular bin-averaged covariances with the flat sky approximation, which are sufficiently accurate for inferring cosmological parameters. The code CosmoCov for computing the real-space covariances with or without the flat-sky approximation is released along with this paper.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Computing virtual dark-field X-ray microscopy images of complex discrete dislocation structures from large-scale molecular dynamics simulations

Dark-field X-ray microscopy (DFXM) is a novel diffraction-based imaging technique that non-destructively maps the local deformation from crystalline defects in bulk materials. While studies have demonstrated that DFXM can spatially map 3D defect geometries, it is still challenging to interpret DFXM images of the high-dislocation-density systems relevant to macroscopic crystal plasticity. This work develops a scalable forward model to calculate virtual DFXM images for complex discrete dislocation structure(s) (DDS) obtained from atomistic simulations. Our new DDS-DFXM model integrates a non-singular formulation for calculating the local strain from the DDS and an efficient geometrical optics algorithm for computing the DFXM image from the strain field. We apply the model to complex DDS obtained from a large-scale molecular dynamics simulation of compressive loading on single-crystal silicon. Simulated DFXM images exhibit prominent contrast for dislocation features between the multiple slip systems, demonstrating the potential of DFXM to resolve features from dislocation multiplication. In conclusion, the integrated DDS-DFXM model provides a toolbox for DFXM experimental design and image interpretation in the context of bulk crystal plasticity for a range of measurements across shock plasticity and the broader materials science community.

X-ray imaging↗

DOE OSTI2023

Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease

Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

WRF Output from 270m domain running simulation with no 3D morphology, NUDAPT 3D morphology, 100m resolution 3D morphology and 10m resolution 3D morphology

This is a group of four datasets that were run for an experiment testing the effect of the resolution and the coverage of 3D urban morphological inputs on meteorological output. This data is associated with the paper "Sensitivity of Urban Morphology to the Resolution of Urban Morphological Feature Inputs: Implications for Characterizing Urban Sustainability."

integrated multisector multiscale modeling↗

DOE OSTI2024

WRF Output from 270m domain running simulation with no 3D morphology, NUDAPT 3D morphology, 100m resolution 3D morphology and 10m resolution 3D morphology

integrated multisector multiscale modeling↗

DOE OSTI2022

Development and performance of a HemeLB GPU code for human-scale blood flow simulation

In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated partition, whilst in others they are integral to all compute nodes - often with multiple GPUs per node - and provide the majority of a machine's compute performance. In light of this trend, it is becoming essential that codes deployed on HPC are updated to execute on accelerator hardware. Here, in this paper, we introduce a GPU implementation of the 3D blood flow simulation code HemeLB that has been developed using CUDA C++. We demonstrate how taking advantage of NVIDIA GPU hardware can achieve significant performance improvements compared to the equivalent CPU only code on which it has been built whilst retaining the excellent strong scaling characteristics that have been repeatedly demonstrated by the CPU version. With HPC positioned on the brink of the exascale era, we use HemeLB as a motivation to provide a discussion on some of the challenges that many users will face when deploying their own applications on upcoming exascale machines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Detector Tilt Considerations in Bragg Coherent Diffraction Imaging: A Simulation Study

This paper addresses the three-dimensional signal distortion and image reconstruction issues in X-ray Bragg coherent diffraction imaging (BCDI) in the event of a general non-orthogonal orientation of the area detector with respect to the diffracted beam. Growing interest in novel BCDI adaptations at fourth-generation synchrotron light sources has necessitated improvisations in the experimental configuration and the subsequent data analysis. One such possibly unavoidable improvisation that is envisioned in this paper is a photon-counting area detector whose face is tilted away from the perpendicular to the Bragg-diffracted beam during the acquisition of the coherent diffraction signal. We describe a likely circumstance in which one would require such a detector configuration, along with the experimental precedent at third-generation synchrotrons. Using physically accurate diffraction simulations from synthetic scatterers in the presence of such tilted detectors, we analyze the general nature of the observed signal distortion qualitatively and quantitatively and provide a prescription to correct for it during image reconstruction. Our simulations and reconstructions are based on an adaptation of the known theory of BCDI sampling geometry, as well as the recently developed projection-based methods of wavefield propagation. Such configurational modifications and their numerical remedies are potentially valuable in realizing unconventional coherent diffraction measurement geometries, eventually paving the way for the integration of BCDI into new material characterization experiments at next-generation light sources.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Resolving ECRH deposition broadening due to edge turbulence in DIII-D

Microwave heat pulse propagation experiments have demonstrated a correlation between millimeter-scale turbulence and deposition profile broadening of electron cyclotron (EC) waves on the DIII-D tokamak. In a set of discharges in DIII-D, a variation in edge density fluctuations on the mm-scale is associated with 40%–150% broader deposition profiles, expressed in terms of normalized minor radius, as compared with equilibrium ray tracing. The 1D power profile is determined from transport analysis of the electron temperature response to EC power modulation using perturbative analysis with a square wave power modulation at 20–70 Hz, producing a series of Fourier harmonics that are fit collectively to resolve transport. Fitting an integrated heat flux expressed in the Fourier basis of the modulation to diffusive, convective, and coupled transport terms in a linear model can resolve the broadened EC deposition width from the power perturbation to resolve a broadening in each case. The best fit degree of beam broadening observed scales approximately linearly with the Doppler backscattering measured fluctuation level in the steep gradient region. Quantifying the effect of edge fluctuation broadening on EC current drive power needs of future devices will require 3D full-wave codes that can be validated on the current generation of machines. These DIII-D experiments provide a quantitative measure of fluctuation effects and a dataset to benchmark full-wave simulations that can model and eventually predict nonlinear effects neglected by 1D equilibrium beam and ray tracing.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Microstructure and water absorption of ancient concrete from Pompeii: An integrated synchrotron microtomography and neutron radiography characterization

There is renewed interest in using advanced techniques to characterize ancient Roman concrete due to its exceptional durability and low-carbon footprint. In the present work, samples were drilled from the “Hospitium” in Pompeii and were analyzed by synchrotron microtomography (μCT) and neutron radiography to study how the microstructure, including the presence of induced cracks, affects their water adsorption. The water distribution and absorptivity were quantified by neutron radiography. The 3D crack propagation, pore size distribution and orientation, tortuosity, and connectivity were analyzed from μCT results using advanced imaging methods. Porosity was also measured by mercury intrusion porosimetry (MIP) as a reference. Ductile fracture patterns were observed once cracks were introduced. Compared to Portland cement mortar/concrete, the Pompeii samples had relatively high porosity, low connectivity, and a similar coefficient of capillary penetration. In addition, permeability was predicted from models based on percolation theory and pore structure data to evaluate the fluid transport properties. Understanding the microstructure of ancient Pompeii concrete is important because it could inspire the development of modern concrete with high durability.

36 MATERIALS SCIENCE↗

DOE OSTI2025

TorchBraid: High-Performance Layer-Parallel Training of Deep Neural Networks with MPI and GPU Acceleration

TorchBraid is a high-performance implementation of layer-parallel training for deep neural networks (DNNs) supporting MPI-based parallelism and GPU acceleration. Layer-parallel training has been developed to overcome the serialization inherent in forward and backward propagation of DNNs that limits utilization of computational resources in the strong scaling limit. To achieve this, TorchBraid integrates the PyTorch neural network framework with the state-of-the-art XBraid time-parallel library. Furthermore, this article presents the use and performance of TorchBraid, in addition to solutions for overcoming the algorithmic challenges inherent in combining automatic differentiation with layer-parallel. Results are presented with and without GPU acceleration for the Tiny ImageNet and MNIST image classification data sets, as well as recurrent neural networks. Overall, TorchBraid enables fast training of DNNs, both in a strong and weak scaling context. In addition to the TorchBraid software, several new advances in applying layer-parallel algorithms are detailed. Integration of layer-parallel with data-parallel algorithms is presented for the first time, showing the computational advantages of the combination. Standard deep learning techniques, like batch-normalization, are developed for layer-parallel training. Finally, a new approach combining layer-parallel with spatial coarsening in order to accelerate training for 3D image classification shows roughly a 10× speedup over serial execution.

Layer-parallel↗

DOE OSTI2021

The Applicability of Unit Systems to High-Performance Computing Applications

Dimensional analysis is a key technique used to verify the soundness of scientific models. Most experts agree that engineering and scientific software would be made more reliable by integrating dimensional analysis in their type system. We explored how High Performance Computing (HPC) applications could integrate compile-time dimensional analysis. We started by investigating various implementation of unit systems for C++. Eventually, selecting the latest (and most advanced) one to apply to our test codes. We worked with code of increasing complexity, from a projectile trajectory calculation to the proxy-application Lulesh. This included our code, Springs-3D, which focuses on demonstrating language features while performing simple physic computations. Finally, our main contribution is a source-code analysis which extracts constraints on the dimension of all variables, functions, and constants in an application. This resulting system of equations is solved using the dimensions of a few of these objects. This analysis has the potential to greatly reduce the time spent performing dimensional analysis when refactoring application to use a representation of units.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Toolpath Optimization of Polymer Composite Additive Manufacturing AM Printed Mold to Improve Performance for Compression Molding Applications

This study explores the optimization of toolpaths for short fiber polymer composite additive manufacturing (AM) printed molds in compression molding applications, an emerging trend driven by advancements in 3D printing technology. AM printed molds offer reduced tooling costs and greater design flexibility, particularly for prototyping and low-volume production. The proposed optimization approach evaluates mold performance using two key metrics: deformation and shape accuracy. Multiple toolpaths are generated, and finite element (FE) simulations capture fiber orientation and material properties, which are then integrated into a mechanical performance model. Shape accuracy is assessed by comparing the deformed mold shape with the original using surface normals as a descriptor. The analysis identifies the toolpath that delivers the best overall performance, establishing it as the most suitable option for achieving optimal mold characteristics in compression molding applications.

Limaye, Madhura [ORNL]↗