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All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2024

Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS

Type 1 polyketides are a major class of natural products used as antiviral, antibiotic, antifungal, antiparasitic, immunosuppressive, and antitumor drugs. Analysis of public microbial genomes leads to the discovery of over sixty thousand type 1 polyketide gene clusters. However, the molecular products of only about a hundred of these clusters are characterized, leaving most metabolites unknown. Characterizing polyketides relies on bioactivity-guided purification, which is expensive and time-consuming. To address this, we present Seq2PKS, a machine learning algorithm that predicts chemical structures derived from Type 1 polyketide synthases. Seq2PKS predicts numerous putative structures for each gene cluster to enhance accuracy. The correct structure is identified using a variable mass spectral database search. Benchmarks show that Seq2PKS outperforms existing methods. Applying Seq2PKS to Actinobacteria datasets, we discover biosynthetic gene clusters for monazomycin, oasomycin A, and 2-aminobenzamide-actiphenol.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Molecular properties of excited electronic state: Formalism, implementation, and applications of analytical second energy derivatives within the framework of the time-dependent density functional theory/molecular mechanics

This work extends our previous works [J. Liu and W. Z. Liang, J. Chem. Phys. 135, 014113 (2011); J. Liu and W. Z. Liang, J. Chem. Phys. 135, 184111 (2011)] on analytical excited-state energy Hessian within the framework of time-dependent density functional theory (TDDFT) to couple with molecular mechanics (MM). The formalism, implementation, and applications of analytical first and second energy derivatives of TDDFT/MM excited state with respect to the nuclear and electric perturbations are presented. Their performances are demonstrated by the calculations of adiabatic excitation energies, and excited-state geometries, harmonic vibrational frequencies, and infrared intensities for a number of benchmark systems. The consistent results with the full quantum mechanical method and other hybrid theoretical methods indicate the reliability of the current numerical implementation of developed algorithms. The computational accuracy and efficiency of the current analytical approach are also checked and the computational efficient strategies are suggested to speed up the calculations of complex systems with many MM degrees of freedom. Finally, we apply the current analytical approach in TDDFT/MM to a realistic system, a red fluorescent protein chromophore together with part of its nearby protein matrix. The calculated results indicate that the rearrangement of the hydrogen bond interactions between the chromophore and the protein matrix is responsible for the large Stokes shift.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Adaptive Quantum Generative Training using an Unbounded Loss Function

We propose a generative quantum learning algorithm using the Adaptive Derivative-Assembled Problem Tailored ansatz (ADAPT) framework in which the loss function to be minimized is the maximal quantum Rényi divergence of order two, an unbounded function that mitigates barren plateaus which inhibit training variational circuits. We benchmark this method against other state-of-the-art adaptive algorithms by learning random two-local thermal states. We perform numerical experiments of up to 12 qubits comparing our method learning algorithms that use linear objective functions and show that Rényi-ADAPT is capable of constructing shallow quantum circuits competitive with existing methods, while the gradients remain favorable resulting from the maximal Rényi divergence loss function.

quantum algorithms, quantum machine learning, quan↗
NASA NTRS1991

A globally well-posed finite element algorithm for aerodynamics applications

A finite element CFD algorithm is developed for Euler and Navier-Stokes aerodynamic applications. For the linear basis, the resultant approximation is at least second-order-accurate in time and space for synergistic use of three procedures: (1) a Taylor weak statement, which provides for derivation of companion conservation law systems with embedded dispersion-error control mechanisms; (2) a stiffly stable second-order-accurate implicit Rosenbrock-Runge-Kutta temporal algorithm; and (3) a matrix tensor product factorization that permits efficient numerical linear algebra handling of the terminal large-matrix statement. Thorough analyses are presented regarding well-posed boundary conditions for inviscid and viscous flow specifications. Numerical solutions are generated and compared for critical evaluation of quasi-one- and two-dimensional Euler and Navier-Stokes benchmark test problems.

Iannelli, G. S.↗
NASA NTRS2006

Simulation Modeling and Performance Evaluation of Space Networks

In space exploration missions, the coordinated use of spacecraft as communication relays increases the efficiency of the endeavors. To conduct trade-off studies of the performance and resource usage of different communication protocols and network designs, JPL designed a comprehensive extendable tool, the Multi-mission Advanced Communications Hybrid Environment for Test and Evaluation (MACHETE). The design and development of MACHETE began in 2000 and is constantly evolving. Currently, MACHETE contains Consultative Committee for Space Data Systems (CCSDS) protocol standards such as Proximity-1, Advanced Orbiting Systems (AOS), Packet Telemetry/Telecommand, Space Communications Protocol Specification (SCPS), and the CCSDS File Delivery Protocol (CFDP). MACHETE uses the Aerospace Corporation s Satellite Orbital Analysis Program (SOAP) to generate the orbital geometry information and contact opportunities. Matlab scripts provide the link characteristics. At the core of MACHETE is a discrete event simulator, QualNet. Delay Tolerant Networking (DTN) is an end-to-end architecture providing communication in and/or through highly stressed networking environments. Stressed networking environments include those with intermittent connectivity, large and/or variable delays, and high bit error rates. To provide its services, the DTN protocols reside at the application layer of the constituent internets, forming a store-and-forward overlay network. The key capabilities of the bundling protocols include custody-based reliability, ability to cope with intermittent connectivity, ability to take advantage of scheduled and opportunistic connectivity, and late binding of names to addresses. In this presentation, we report on the addition of MACHETE models needed to support DTN, namely: the Bundle Protocol (BP) model. To illustrate the use of MACHETE with the additional DTN model, we provide an example simulation to benchmark its performance. We demonstrate the use of the DTN protocol and discuss statistics gathered concerning the total time needed to simulate numerous bundle transmissions

network protocols↗
NASA NTRS2006

Delay Tolerant Networking - Bundle Protocol Simulation

In this paper, we report on the addition of MACHETE models needed to support DTN, namely: the Bundle Protocol (BP) model. To illustrate the useof MACHETE with the additional DTN model, we provide an example simulation to benchmark its performance. We demonstrate the use of the DTN protocol and discuss statistics gathered concerning the total time needed to simulate numerous bundle transmissions.

licklider protocol↗
NASA NTRS2012

Alternative Modal Basis Selection Procedures For Reduced-Order Nonlinear Random Response Simulation

Three procedures to guide selection of an efficient modal basis in a nonlinear random response analysis are examined. One method is based only on proper orthogonal decomposition, while the other two additionally involve smooth orthogonal decomposition. Acoustic random response problems are employed to assess the performance of the three modal basis selection approaches. A thermally post-buckled beam exhibiting snap-through behavior, a shallowly curved arch in the auto-parametric response regime and a plate structure are used as numerical test articles. The results of a computationally taxing full-order analysis in physical degrees of freedom are taken as the benchmark for comparison with the results from the three reduced-order analyses. For the cases considered, all three methods are shown to produce modal bases resulting in accurate and computationally efficient reduced-order nonlinear simulations.

Przekop, Adam↗
DOE OSTI2012

The Method of Manufactured Solutions for RattleSnake A SN Radiation Transport Solver Inside the MOOSE Framework

The Method of Manufactured Solutions (MMS) is an accepted technique to verify that a numerical discretization for the radiation transport equation has been implemented correctly. This technique offers a few advantages over other methods such as benchmark problems or analytical solutions. The solution can be manufactured such that properties for the angular flux are either stressed or preserved. For radiation transport, these properties can include desired smoothness, positiveness and arbitrary order of anisotropy in angle. Another advantage is that the angular flux solution can be manufactured for multidimensional problems where analytical solutions are difficult to obtain in general.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2015

A spectral scheme for Kohn–Sham density functional theory of clusters

Starting from the observation that one of the most successful methods for solving the Kohn–Sham equations for periodic systems – the plane-wave method – is a spectral method based on eigenfunction expansion, we formulate a spectral method designed towards solving the Kohn–Sham equations for clusters. This allows for efficient calculation of the electronic structure of clusters (and molecules) with high accuracy and systematic convergence properties without the need for any artificial periodicity. The basis functions in this method form a complete orthonormal set and are expressible in terms of spherical harmonics and spherical Bessel functions. Computation of the occupied eigenstates of the discretized Kohn–Sham Hamiltonian is carried out using a combination of preconditioned block eigensolvers and Chebyshev polynomial filter accelerated subspace iterations. Several algorithmic and computational aspects of the method, including computation of the electrostatics terms and parallelization are discussed. We have implemented these methods and algorithms into an efficient and reliable package called ClusterES (Cluster Electronic Structure). A variety of benchmark calculations employing local and non-local pseudopotentials are carried out using our package and the results are compared to the literature. Convergence properties of the basis set are discussed through numerical examples. Computations involving large systems that contain thousands of electrons are demonstrated to highlight the efficacy of our methodology. The use of our method to study clusters with arbitrary point group symmetries is briefly discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

The experiment filtering tool in the MACSENS workbench - 14341

The MACSENS (outils Moret d'Aide a la Caracterisation et aux etudes de SENSibilite) workbench is dedicated to the advanced validation work for criticality studies. The aim of this kind of tool is to determine the experiments from a validation database being the 'closest' to an application case and, from there, to evaluate a calculation bias with a related uncertainty. To achieve this goal, the MACSENS workbench relies on different kind of information stored in various databases depending on the origin of the data. Two main kinds of data can be identified. The first one concerns the data used to describe the experiments of the validation database (e.g. the inputs needed to perform a calculation). These values characterize the chemical and geometrical models. They can be considered as constant, as they do not vary once evaluated, and some of them can be from a non-numerical nature (reflector material for example...). The second kind of data gathers the results obtained with the use of a simulation code, such as reaction rates, fluxes and leakages, sensitivities, k{sub eff}, etc. These values depend on the version of the code and are purely numerical. In the early 2000's, regarding the increasing number of experiments evaluated in the ICSBEP handbook, the OECD/NEA (Organization for Economic Co-operation and Development/Nuclear Energy Agency), under the ICSBEP (International Criticality Safety Benchmark Evaluation Project) working group direction, decided to store such information in a database and to provide a software, called DICE (Database for the International Criticality safety benchmark Evaluation project), allowing users to search easily criticality experiments of interest. Up to now, more than 4400 critical or subcritical configurations have been compiled by ICSBEP, described and stored in the DICE database. Over time, a validation work has been done on the data, with the participation of IRSN, and a quality assurance policy has been defined. For these reasons, the DICE database is highly reliable. These features were fundamental for the MACSENS developers, who were looking for a database containing descriptive data of the experiments included in the MORET code validation database. The paper describes the solution chosen by IRSN to take advantage of the DICE database content and to overcome the DICE limits. It also explains the quality assurance policy applied to guaranty the reliability of the stored data. It will also discuss the use of the experiment-filtering module of the MACSENS workbench to select a set of experiments and to examine numerical parameter trends for an application case. (authors)

42 ENGINEERING↗
DOE OSTI2025

Benchmark study of the DTU OWC chamber with both two-way and one-way absorption

This paper reports on a benchmark study based on small-scale (1:50) measurements of a single, oscillating water column chamber mounted sideways in a long flume. The geometry of the OWC chamber is extracted from a barge-like, attenuator-type floating concept “KNSwing” with 40 chambers targeted for deployment in the Danish part of the North Sea. In addition to traditional two-way energy extraction we also consider one-way energy extraction with passive venting and compare chamber response, pressures and total absorbed energy between the two methods. A blind study was established for the numerical modeling, with participants applying several implementations of weakly nonlinear potential flow theory and commercial Navier–Stokes solvers (CFD). Both compressible and incompressible models were used for the air phase. Potential flow calculations predict more energy absorption near the chamber resonance for one-way absorption than for two-way absorption, but the opposite is found from the experimental measurements. This outcome is mainly attributed to energy losses in the experimental passive valve system, but this conclusion must be confirmed by better experimental measurements. Modeling the one-way valve in CFD proved to be very challenging and only one team was able to provide results which were generally closer to the experiments. The study illustrates the challenges associated with both numerical and experimental analysis of OWC chambers. Air compressibility effects were not found to be important at this scale, even with the large volume of additional air used for the one-way case.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

HamLib: A Library of Hamiltonians for Benchmarking Quantum Algorithms and Hardware

For a considerable time, large datasets containing problem instances have proven valuable for analyzing computer hardware, software, and algorithms. One notable example of the value of large datasets is ImageNet [1], a vast repository of images that has been instrumental in testing numerous deep learning packages. Similarly, in the domain of computational chemistry and materials science, the availability of extensive datasets such as the Protein Data Bank [2], the Materials Project [3], and QM9 [4] has greatly facilitated the evaluation of new algorithms and software approaches, while also promoting standardization within the field. These well-defined datasets and problem instances, in turn, serve as the foundation for creating benchmarking suites like MLPerf [5] and LINPACK [6], [7]. These suites enable fair and rigorous comparisons of different methodologies and solutions, fostering continuous advancements in various areas of computer science and beyond.

Sawaya, Nicolas PD↗
DOE OSTI2014

TH-E-BRE-01: A 3D Solver of Linear Boltzmann Transport Equation Based On a New Angular Discretization Method with Positivity for Photon Dose Calculation Benchmarked with Geant4

Purpose: The Linear Boltzmann Transport Equation (LBTE) solved through statistical Monte Carlo (MC) method provides the accurate dose calculation in radiotherapy. This work is to investigate the alternative way for accurately solving LBTE using deterministic numerical method due to its possible advantage in computational speed from MC. Methods: Instead of using traditional spherical harmonics to approximate angular scattering kernel, our deterministic numerical method directly computes angular scattering weights, based on a new angular discretization method that utilizes linear finite element method on the local triangulation of unit angular sphere. As a Result, our angular discretization method has the unique advantage in positivity, i.e., to maintain all scattering weights nonnegative all the time, which is physically correct. Moreover, our method is local in angular space, and therefore handles the anisotropic scattering well, such as the forward-peaking scattering. To be compatible with image-guided radiotherapy, the spatial variables are discretized on the structured grid with the standard diamond scheme. After discretization, the improved sourceiteration method is utilized for solving the linear system without saving the linear system to memory. The accuracy of our 3D solver is validated using analytic solutions and benchmarked with Geant4, a popular MC solver. Results: The differences between Geant4 solutions and our solutions were less than 1.5% for various testing cases that mimic the practical cases. More details are available in the supporting document. Conclusion: We have developed a 3D LBTE solver based on a new angular discretization method that guarantees the positivity of scattering weights for physical correctness, and it has been benchmarked with Geant4 for photon dose calculation.

97 MATHEMATICS AND COMPUTING↗