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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Kernel-based global sensitivity analysis obtained from a single data set

Results from global sensitivity analysis (GSA) often guide the understanding of complicated input–output systems. Kernel-based GSA methods have recently been proposed for their capability of treating a broad scope of complex systems. In this paper, we develop a new set of kernel GSA tools when only a single set of input–output data is available. Three key advances are made: (1) A new numerical estimator is proposed that demonstrates an empirical improvement over previous procedures. (2) A computational method for generating inner statistical functions from a single data set is presented. (3) A theoretical extension is made to define conditional sensitivity indices, which reveal the degree that the inputs carry shared information about the output when inherent input–input correlations are present. Utilizing these conditional sensitivity indices, a decomposition is derived for the output uncertainty based on what is called the optimal learning sequence of the input variables, which remains consistent when correlations exist between the input variables. Further, while these advances cover a range of GSA subjects, a common single data set numerical solution is provided by a technique known as the conditional mean embedding of distributions. The new methodology is implemented on benchmark systems to demonstrate the provided insights.

42 ENGINEERING↗
DOE OSTI2025

Assessing the potential of deep learning for protein–ligand docking

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.

Morehead, Alex [Lawrence Berkeley National Laborat↗
DOE OSTI2014

Communication: Four-component density matrix renormalization group

We present the first implementation of the relativistic quantum chemical two- and four-component density matrix renormalization group algorithm that includes a variational description of scalar-relativistic effects and spin–orbit coupling. Numerical results based on the four-component Dirac–Coulomb Hamiltonian are presented for the standard reference molecule for correlated relativistic benchmarks: thallium hydride.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Correlation consistent basis sets for explicitly correlated wavefunctions: Pseudopotential-based basis sets for the post-d main group elements Ga–Rn

New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga–Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of the spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Modeling of resistive plasma response in toroidal geometry using an asymptotic matching approach

The method of solving the linear resistive plasma response, based on the asymptotic matching approach, is developed for full toroidal tokamaks by upgrading the resistive DCON code [A. H. Glasser, Z. R. Wang, and J.-K. Park, Phys. Plasmas 23, 112506 (2016)]. The derived matching matrix, asymptotically matching the outer and inner regions, indicates that the applied three dimension (3-D) magnetic perturbations contribute additional small solutions at each resonant surface due to the toroidal coupling of poloidal modes. In contrast, the resonant harmonic only affects the corresponding resonant surface in the cylindrical plasma. Additionally, the solution of the ideal outer region is critical to the asymptotic matching and is challenging in toroidal geometry due to the singular power series solution at the resonant surfaces. Thus, a systematic verification of the outer region Δ' matrix is made by reproducing the well-known analytical Δ' result in Furth et al. [Phys. Fluids 16, 1054–1063 (1073)] and by making a quantitative benchmark with the PEST3 code [A. Pletzer and R. L. Dewar, J. Plasma Phys. 45, 427–451 (1991)]. Finally, the reconstructed numerical solution of the resistive plasma response from the toroidal matching matrix is presented. Compared with the ideal plasma response, the global structure of the response can be affected by the small finite island at the resonant surfaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

MAS: A versatile Landau-fluid eigenvalue code for plasma stability analysis in general geometry

We have developed a new global eigenvalue code, Multiscale Analysis for plasma Stabilities (MAS), for studying plasma problems with wave toroidal mode number (n) and frequency (ω) in a broad range of interest in general tokamak geometry, based on a five-field Landau-fluid description of thermal plasmas. Beyond keeping the necessary plasma fluid response, we further retain the important kinetic effects including diamagnetic drift, ion finite Larmor radius, finite parallel electric field (E||), ion and electron Landau resonances in a self-consistent and non-perturbative manner without sacrificing the attractive efficiency in computation. The physical capabilities of the code are evaluated and examined in the aspects of both theory and simulation. In theory, the comprehensive Landau-fluid model implemented in MAS can be reduced to the well-known ideal MHD model, electrostatic ion-fluid model, and drift-kinetic model in various limits, which clearly delineates the physics validity regime. In simulation, MAS has been well benchmarked with theory and other gyrokinetic and kinetic-MHD hybrid codes in a manner of adopting the unified physical and numerical framework, which covers the kinetic Alfv\'en wave (KAW), ion sound wave (ISW), low-n kink, high-n ion temperature gradient mode (ITG) and kinetic ballooning mode (KBM). Moreover, MAS is successfully applied to model the Alfv\'en eigenmode (AE) activities in DIII-D discharge #159243, which faithfully captures the frequency sweeping of reversed shear Alfv\'en eigenmode (RSAE), the tunneling damping of toroidal Alfv\'en eigenmode (TAE), as well as the polarization characteristics of kinetic beta-induced Alfv\'en eigenmode (KBAE) and beta-induced Alfv\'en-acoustic eigenmode (BAAE) being consistent with former gyrokinetic theory and simulation. With respect to the key progress contributed to the community, MAS has the advantage of combining rich physics ingredients, realistic global geometry and high computation efficiency together for plasma stability analysis in linear regime.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Compressing deep neural networks on FPGAs to binary and ternary precision with hls4ml

We present the implementation of binary and ternary neural networks in the hls4ml library, designed to automatically convert deep neural network models to digital circuits with FPGA firmware. Starting from benchmark models trained with floating point precision, we investigate different strategies to reduce the network's resource consumption by reducing the numerical precision of the network parameters to binary or ternary. We discuss the trade-off between model accuracy and resource consumption. In addition, we show how to balance between latency and accuracy by retaining full precision on a selected subset of network components. As an example, we consider two multiclass classification tasks: handwritten digit recognition with the MNIST data set and jet identification with simulated proton-proton collisions at the CERN Large Hadron Collider. The binary and ternary implementation has similar performance to the higher precision implementation while using drastically fewer FPGA resources.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

Acausality-driven instabilities in relativistic viscous hydrodynamics

We investigate non-linear instabilities stemming from superluminal propagation of information in Israel-Stewart-like models of relativistic viscous fluid dynamics. In relativity, the characteristic speed of propagation of information, $w$, and the speed of the fluid, $v$, allow us to differentiate between regimes of the hydrodynamic equations that are acausal but stable ($w>1$), unstable ($v^{2} w^{2} \geq 1$), and covariantly ill-posed ($w^{2} \leq 0$). As an analytical benchmark, we present a new solution that illustrates these distinct regimes. We compare this analytical solution to the result of a numerical relativistic viscous fluid dynamics solver, and confirm that the analytical result can be recovered numerically in the stable regime, whether causal or acausal. The onset of numerical instabilities is further found to occur in the regime predicted by the analytical solution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Modeling of resistive plasma response in toroidal geometry using an asymptotic matching approach

The method of solving linear resistive plasma response, based on the asymptotic matching approach, is developed for full toroidal tokamaks by upgrading the Resistive DCON code [A.H. Glasser, Z.R. Wang and J.-K. Park, Physics of Plasmas, \textbf{23}, 112506 (2016)]. The derived matching matrix, asymptotically matching the outer and inner regions, indicates that the applied three dimension (3-D) magnetic perturbations contribute additional small solutions at each resonant surface due to the toroidal coupling of poloidal modes. In contrast, the resonant harmonic only affects the corresponding resonant surface in the cylindrical plasma. Since the solution of ideal outer region is critical to the asymptotic matching and is challenging to be solved in the toroidal geometry due to the singular power series solution at the resonant surfaces, systematic verification of the outer region $\Delta^\prime$ matrix is made by reproducing the well known analytical $\Delta^{\prime}$ result in [H.P. Furth, P.H. Rutherford and H. Selberg, The Physics of Fluids, \textbf{16}, 1054-1063 (1073)] as well as by making a quantitative benchmark with the PEST3 code [A. Pletzer and R.L. Dewar, J. Plasma Physics, \textbf{45}, 427-451 (1991)]. Finally, the reconstructed numerical solution of resistive plasma response from the toroidal matching matrix is presented. Comparing with the ideal plasma response, the global structure of the response can be affected by the small finite island at the resonant surfaces.

MHD simulation↗
DOE OSTI2021

Multi-Area Distribution System State Estimation Using Decentralized Physics-Aware Neural Networks

The development of active distribution grids requires more accurate and lower computational cost state estimation. In this paper, the authors investigate a decentralized learning-based distribution system state estimation (DSSE) approach for large distribution grids. The proposed approach decomposes the feeder-level DSSE into subarea-level estimation problems that can be solved independently. The proposed method is decentralized pruned physics-aware neural network (D-P2N2). The physical grid topology is used to parsimoniously design the connections between different hidden layers of the D-P2N2. Monte Carlo simulations based on one-year of load consumption data collected from smart meters for a three-phase distribution system power flow are developed to generate the measurement and voltage state data. The IEEE 123-node system is selected as the test network to benchmark the proposed algorithm against the classic weighted least squares and state-of-the-art learning-based DSSE approaches. Numerical results show that the D-P2N2 outperforms the state-of-the-art methods in terms of estimation accuracy and computational efficiency.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Jas4pp — A data-analysis framework for physics and detector studies

This paper describes the Jas4pp framework for exploring physics cases and for detector-performance studies of future particle collision experiments. Jas4pp is a multi-platform Java program for numeric calculations, scientific visualization in 2D and 3D, storing data in various file formats and displaying collision events and detector geometries. It also includes complex data-analysis algorithms for function minimization, regression analysis, event reconstruction (such as jet reconstruction), limit settings and other libraries widely used in particle physics. The framework can be used with several scripting languages, such as Python/Jython, Groovy and JShell. Several benchmark tests discussed in the paper illustrate significant improvements in the performance of the Groovy and JShell scripting languages compared to the standard Python implementation in C. Furthermore, the improvements for numeric computations in Java are attributed to recent enhancements in the Java Virtual Machine.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Verification and Validation of CFD Simulations involving Twin Rectangular Jets using Steady RANS in Star-CCM+

Analyses such as component design and safety analysis can be conducted through careful application of computational fluid dynamics (CFD) codes. Before these codes can be considered ready for specific analysis, benchmarking (validation) against applicable datasets is needed. The twin jet water facility (TJWF) developed originally at the University of Tennessee, Knoxville has been purposed for aiding in this type of work. The TJWF allows for large data sets to be created using state of the art non-invasive measurement techniques within a mostly transparent testing volume. Utilizing velocity data collected in the TJWF by Wang et. al., the Star-CCM+ code was benchmarked a using steady Reynolds averaged Navier Stokes (RANS) framework for a combining two jet case. Careful efforts to properly conduct verification of the numerical work was undertaken with a sample reported in this summary. The computational results were validated against the experimental work and found to be within acceptable limits. The parameters of interest were the merging and combining points (MP and CP) of the twin jets, and the velocity profiles at increasing heights after injection. Fig.1 provides a graphical depiction of the twin jets combining within a free shear volume with key geometric factors included. The MP and velocity profiles were predicted with reasonable agreement. Whereas, the combining point of the twin jets was found to be over-predicted by {approx}24% difference. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2016

Reinvestigation into Closure Predictions of Room D at the Waste Isolation Pilot Plant

Room D was an in-situ, isothermal, underground experiment conducted at the Waste Isolation Pilot Plant between 1984 and 1991. The room was carefully instrumented to measure the horizontal and vertical closure immediately upon excavation and for several years thereafter. Early finite element simulations of salt creep around Room D under-predicted the vertical closure by 4.5×, causing investigators to explore a series of changes to the way Room D was modeled. Discrepancies between simulations and measurements were resolved through a series of adjustments to model parameters, which were openly acknowledged in published reports. Interest in Room D has been rekindled recently by the U.S./German Joint Project III and Project WEIMOS, which seek to improve the predictions of rock salt constitutive models. Joint Project participants calibrate their models solely against laboratory tests, and benchmark the models against underground experiments, such as room D. This report describes updating legacy Room D simulations to today’s computational standards by rectifying several numerical issues. Subsequently, the constitutive model used in previous modeling is recalibrated two different ways against a suite of new laboratory creep experiments on salt extracted from the repository horizon of the Waste Isolation Pilot Plant. Simulations with the new, laboratory-based, calibrations under-predict Room D vertical closure by 3.1×. A list of potential improvements is discussed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

DECOVALEX-2023: Task G, SAFENET Final Report

DECOVALEX Task G deals with fracture mechanics at several scales using a combined approach of experimental work, related model development, benchmarking and experimental analysis. Fig. 0.1 provides a graphical abstract for Task G. The experimental basis for the related mechanical (M), hydro-mechanical (HM), and thermo-mechanical (TM) processes comes from the rock mechanics laboratories of Universities of Freiberg (TUBAF) and Edinburgh, as well as the Korea Institute of Civil Engineering and Building Technology (KICT). The experimental work in the rock laboratories is closely linked to the underground research laboratories (URLs) Reiche Zeche (Germany), KURT (Korea), and Mont Terri (Switzerland). The scientific key questions are related to fracture permeability evolution under THM conditions, anisotropy effects on fracturing processes, and thermal fracture slip, which are being addressed in specific steps of the task. A large variety of numerical methods have been developed and applied for experimental analysis, ranging from continuum to discontinuum approaches. A detailed comparison of mechanical and hydro-mechanical processes is given in the section 3 via the benchmarking exercises. As a result of DECOVALEX-2023 Task G we further improved our understanding and predictability of fracturing processes under THM conditions. This was based on robust numerical simulation methods and in-depth experimental analysis.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

A code-to-code benchmark for magneto-convection in a horizontal duct

Liquid metals and magnetic fields are used in many technical applications such as metallurgy, crystal growth and nuclear fusion reactors. When an electrically conducting fluid moves in a magnetic environment, electric currents and electromagnetic forces are generated that affect velocity and pressure losses in the flow. These magnetohydrodynamic (MHD) interactions have to be investigated to optimize the engineering processes. The characteristics of MHD flows depend on the geometrical configuration, the strength of the applied magnetic field, the electrical properties of fluid and structural materials and the thermal conditions. In the so-called blankets for fusion reactors, where liquid metals are used to breed the plasma fuel component tritium and to extract the generated heat, magneto-convective flows play a crucial role in determining heat and mass transfer. Therefore, the availability of numerical codes to simulate this type of flow is mandatory and their validation is a necessary step to guarantee the reliability of the results. For that reason, a benchmark problem has been defined to simulate liquid metal flows in a horizontal rectangular duct heated from below and exposed to a non-uniform magnetic field. Results obtained by five research groups using different codes are compared.

benchmark↗
DOE OSTI2023

Derivation of heterogeneous material distributions and their sensitivity to HM-coupled two-phase flow models exemplified with the LASGIT experiment

Abstract Advective gas transport in bentonite, a possible buffer material in repositories for radioactive materials, is difficult to simulate in numerical continuum models, partly due to the complicated microstructure of bentonite. To generate reliable models of repositories nevertheless, spatially distributed heterogeneous material properties can be used to allow localization of gas flow. In this study, a pore-size-dependent stochastic approach of the gas entry pressure is derived from Mercury Intrusion Porosimetry, which is used to replicate measurements from the LASGIT experiment. In addition, three benchmark tests are simulated to investigate the dependence of heterogeneous distributions of material properties on the mesh discretization, the temporal dependence, and the coupling between the processes influenced by the heterogeneous parameters. The numerical modeling results of the LASGIT experiment show that the onset of gas flow into the system and the subsequent increase in pressure and stress can be well reproduced using heterogeneous distributions. Compared to a model with homogeneous material properties, heterogeneous distributions may allow the generation of dilatancy-controlled microfractures—an important feature with regard to the advective gas flow in bentonites. However, it can be observed that the heterogeneous distributions in LASGIT are less significant, as technical gaps or differences in material types could have a greater impact.

Environmental Sciences & Ecology↗
DOE OSTI2020

Challenges and Opportunities in Magnetospheric Space Weather Prediction

Abstract Space Weather is the study of the dynamics of the coupled Solar‐Terrestrial environment, as these dynamics impact technological systems and human activity. This paper reviews a selection of the advances, challenges, and new opportunities for magnetospheric space weather, and while the focus is on specific phenomena, many other aspects of space weather will have similar challenges and needs. As a scientific field with direct applications, the field of space weather is partly driven by imperatives from both policy and operations. We provide an introduction to some of the context in which the field exists and discuss how this might shape future developments and norms within the space weather enterprise. We briefly examine benchmarking, as a policy and operationally driven activity, as it provides immediate societal relevance and an opportunity to stretch scientific understanding. As numerical space weather prediction now becomes routine, and exascale computing is in the near future, we identify challenges relating to computational expense and big data, capturing and accounting for uncertainties, and specification of boundary conditions. Here, as with the observations supporting numerical space weather prediction, the key challenge lies in extending the lead time of predictions. We also discuss the role of data, particularly in regard to model validation and empirical modeling. Due to the growing societal impact of space weather, we also examine the relationships between space weather and its terrestrial counterpart and look at the importance of continuous evaluation, monitoring progress in predictive capability, and communication with researchers, forecasters, and end users.

79 ASTRONOMY AND ASTROPHYSICS↗