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DOE OSTI2023

hIPPYlib-MUQ: A Bayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty

Bayesian inference provides a systematic framework for integration of data with mathematical models to quantify the uncertainty in the solution of the inverse problem. However, the solution of Bayesian inverse problems governed by complex forward models described by partial differential equations (PDEs) remains prohibitive with black-box Markov chain Monte Carlo (MCMC) methods. We present hIPPYlib-MUQ, an extensible and scalable software framework that contains implementations of state-of-the art algorithms aimed to overcome the challenges of high-dimensional, PDE-constrained Bayesian inverse problems. These algorithms accelerate MCMC sampling by exploiting the geometry and intrinsic low-dimensionality of parameter space via derivative information and low rank approximation. The software integrates two complementary open-source software packages, hIPPYlib and MUQ. hIPPYlib solves PDE-constrained inverse problems using automatically-generated adjoint-based derivatives, but it lacks full Bayesian capabilities. MUQ provides a spectrum of powerful Bayesian inversion models and algorithms, but expects forward models to come equipped with gradients and Hessians to permit large-scale solution. By combining these two complementary libraries, we created a robust, scalable, and efficient software framework that realizes the benefits of each and allows us to tackle complex large-scale Bayesian inverse problems across a broad spectrum of scientific and engineering disciplines. To illustrate the capabilities of hIPPYlib-MUQ, we present a comparison of a number of MCMC methods available in the integrated software on several high-dimensional Bayesian inverse problems. These include problems characterized by both linear and nonlinear PDEs, various noise models, and different parameter dimensions. The results demonstrate that large (~ 50×) speedups over conventional black box and gradient-based MCMC algorithms can be obtained by exploiting Hessian information (from the log-posterior), underscoring the power of the integrated hIPPYlib-MUQ framework.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Reduced order models for thermal radiative transfer problems based on moment equations and data-driven approximations of the Eddington tensor

Here a new group of structure and asymptotic preserving reduced-order models (ROMs) for multidimensional nonlinear thermal radiative transfer (TRT) problems is presented. They are formulated by means of the nonlinear projective approach and data compression techniques. The nonlinear projection is applied to the Boltzmann transport equation (BTE) to derive a hierarchy of low-order moment equations. Approximation of the Eddington tensor that provides exact closure for the system of moment equations is found with projection-based data-driven methodologies. These include the (i) proper orthogonal decomposition (POD), (ii) dynamic mode decomposition (DMD) and (iii) a variant of the DMD. A parameterization is derived for this ROM for the temperature of radiation incoming to the problem domain (the radiation drive temperature). This parameterization is informed from results of a dimensionless study of the TRT problem. Analysis of the ROMs is performed on the classical Fleck-Cummings TRT multigroup test problem in 2D geometry with a radiation-driven Marshak wave. Numerical results are presented to demonstrate the performance of these ROMs for the simulation of evolving radiation and heat waves. Results show these models to be sufficiently accurate for practical computations with rather low-rank representations of the Eddington tensor. As the rank of the approximation is increased, the errors of solutions generated by the ROMs gradually decreases.

42 ENGINEERING↗

DOE OSTI2021

Stability and Conservation properties of Hermite-based approximations of the Vlasov-Poisson System

Spectral approximation based on Hermite-Fourier expansion of the Vlasov-Poisson model for a collisionless plasma in the electro-static limit is provided by adding high-order artificial collision operators of Lenard-Bernstein type. These differential operators are suitably designed in order to preserve the physically-meaningful invariants (number of particles, momentum, energy). In view of time-discretization, stability results in appropriate norms are presented. In this study, necessary conditions link the magnitude of the artificial collision term, the number of spectral modes of the discretization, as well as the time-step. The analysis, carried out in full for the Hermite discretization of a simple linear problem in one-dimension, is then partly extended to cover the complete nonlinear Vlasov-Poisson model.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Multi-species collisions for delta-f gyrokinetic simulations: Implementation and verification with GENE

we report a multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius (FLR) effects have also been implemented into the local version of the code. For the global version of the code, the collision operator has been developed to allow for block-structured velocity space grids, allowing for computationally tractable collisional global simulations. The validity of the collision operator has been demonstrated by relaxation and conservation tests, as well as appropriate benchmarks. The newly implemented operator shall be used in future simulations to study magnetically confined fusion plasma turbulence and transport in more extreme regions with higher collisionality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Multi-species collisions for delta-f gyrokinetic simulations: Implementation and verification with GENE

A multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius (FLR) effects have also been implemented into the local version of the code. For the global version of the code, the collision operator has been developed to allow for block-structured velocity space grids, allowing for computationally tractable collisional global simulations. The validity of the collision operator has been demonstrated by relaxation and conservation tests, as well as appropriate benchmarks. The newly implemented operator shall be used in future simulations to study magnetically confined fusion plasma turbulence and transport in more extreme regions with higher collisionality.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Lagrangian and Eulerian Supersaturation Statistics in Turbulent Cloudy Rayleigh–Bénard Convection: Applications for LES Subgrid Modeling

Abstract Turbulent fluctuations of scalar and velocity fields are critical for cloud microphysical processes, e.g., droplet activation and size distribution evolution, and can therefore influence cloud radiative forcing and precipitation formation. Lagrangian and Eulerian water vapor, temperature, and supersaturation statistics are investigated in direct numerical simulations (DNS) of turbulent Rayleigh–Bénard convection in the Pi Convection Cloud Chamber to provide a foundation for parameterizing subgrid-scale fluctuations in atmospheric models. A subgrid model for water vapor and temperature variances and covariance and supersaturation variance is proposed, valid for both clear and cloudy conditions. Evaluation of phase change contributions through an a priori test using DNS data shows good performance of the model. Supersaturation is a nonlinear function of temperature and water vapor, and relative external fluxes of water vapor and heat (e.g., during entrainment-mixing and phase change) influence turbulent supersaturation fluctuations. Although supersaturation has autocorrelation and structure functions similar to the independent scalars (temperature and water vapor), the autocorrelation time scale of supersaturation differs. Relative scalar fluxes in DNS without cloud make supersaturation PDFs less skewed than the adiabatic case, where they are highly negatively skewed. However, droplet condensation changes the PDF shape response: it becomes positively skewed for the adiabatic case and negatively skewed when the sidewall relative fluxes are large. Condensation also increases correlations between water vapor and temperature in the presence of relative scalar fluxes but decreases correlations for the adiabatic case. These changes in correlation suppress supersaturation variability for the nonadiabatic cases and increase it for the adiabatic case. Implications of this work for subgrid microphysics modeling using a Lagrangian stochastic scheme are also discussed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Skyrmion superconductivity: DMRG evidence for a topological route to superconductivity

It was recently suggested that the topology of magic-angle twisted bilayer graphene's (MATBG) flat bands could provide a novel mechanism for superconductivity distinct from both weakly coupled BCS theory and the d-wave phenomenology of the high-T c cuprates. In this work, we examine this possibility using a density matrix renormalization group (DMRG) study of a model which captures the essential features of MATBG's symmetry and topology. Here, using large-scale cylinder-DMRG calculations to obtain the ground state and its excitations as a function of the electron doping, we find clear evidence for superconductivity driven by the binding of electrons into charge-2e skyrmions. Remarkably, this binding is observed even in the regime where the unscreened Coulomb repulsion is by far the largest energy scale, demonstrating the robustness of this topological, all-electronic pairing mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2024

Testing and modeling of CLT-to-CLT joints made using hardwood dowels and screws with varying spacing

With the increasing popularity of mass timber, utilizing large-diameter wood screws and hardwood dowels can offer an easy and cost-efficient way to join structural elements. However, the existing research on hardwood dowels is limited to single fastener joints under monotonic loading. No research is available on the group effects of joints with multiple hardwood dowels. Here, this paper presents the results of 96 monotonic and cyclic single-shear plane CLT-to-CLT joint tests with hardwood dowels (Red Oak and Yellow Birch, 25.4 mm diameter) and self-tapping wood screws (8 mm diameter) in Grand-Fir CLT, where screws were inserted both perpendicular and at a 45-degree angle to the grain for comparison to hardwood dowels. The study evaluated the mechanical properties of the joints by changing fastener spacing. Mechanical properties such as yielding and peak strength, displacement, elastic and yielding stiffness, and ductility were evaluated. The results showed equal strength and stiffness properties for hardwood dowels comparable with large-diameter screws. Additionally, the hardwood dowel joints demonstrated moderate ductility properties. The strength and stiffness of the tested joints were compared with analytical equations found in the literature by considering the group action factor of the fasteners. Lastly, a nonlinear force-displacement model was presented and compared to the experimental results and analytical calculations, which gives the possibility to predict and optimize the mechanical behavior of hardwood dowel and screw joints with varying numbers and spacing between fasteners.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Discrete Empirical Interpolation Method Based Dynamic Load Model Reduction

Dynamic load models add significant complexity to bulk power system time-domain simulations. The complexity is due to the large number of ordinary differential equations (ODEs) introduced by the dynamic load components such as induction motors. It is challenging to derive reduced-order models (ROMs) for dynamic loads due to the nonlinear functions in their governing equations. This paper applies the discrete empirical interpolation method enhanced proper orthogonal decomposition (DEIM-POD) to approximate the full dynamic load model with the ROM that minimizes the projection error of the nonlinear functions in dynamic load ODEs onto their dominant modes. This approach only requires evaluation of nonlinear functions at selected observation points. The observation points selected by DEIM also provide information for screening critical load buses where dynamic load model parameters contribute the most to the accuracy of ROM across multiple contingencies. The proposed approach is validated on IEEE 9-bus, WECC 179-bus and 2384-bus Polish systems.

bulk power system↗

DOE OSTI2022

Co-optimized machine-learned manifold models for large eddy simulation of turbulent combustion

Many modeling approaches in large eddy simulation (LES) of turbulent combustion employ a projection of the thermochemical state onto a low-dimensional manifold within state space to reduce the number of transported variables and hence computational cost. Flamelet-generated manifolds (FGM) is an example of a well-established, physics-based approach, but increasingly, principal component analysis (PCA) is being used as a data-driven method for generating manifold models. For both approaches, the nonlinear relationship between the location on the predefined manifold and the outputs of interest, such as reaction rates, can be tabulated or encoded in a neural network. This work proposes a new approach for manifold modeling that extends these existing approaches. A modified neural network structure simultaneously encodes the definition of the manifold variables, the nonlinear mapping, and the subfilter closure for LES. This allows all three of these aspects of the model to be co-optimized, generating a model from any source of combustion thermochemical state data. The manifold parameterizing variables are constrained to be linear combinations of species, as in FGM and PCA-based models, to aid in interpretability and implementation. For LES, subfilter variances of the manifold variables are also included as inputs. Two types of a priori analysis are performed to evaluate the new approach. In the first, the model is trained on data from one-dimensional premixed flames. In this case, the approach recovers the behavior of flamelet-based manifold approaches, and in fact slightly improves performance by identifying an optimized progress variable. The approach is also applied to data from direct numerical simulations of spherical ignition kernels in isotropic turbulence. For any specified manifold dimensionality, the new approach provides substantially lower prediction errors than a PCA-based model developed from the same data set. Additionally, the LES formulation of the new approach can provide accurate predictions for filtered reaction rates across a variety of filter widths.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

A Comparison of Interface Growth Models Applied to Rayleigh–Taylor and Richtmyer–Meshkov Instabilities

Sophisticated numerical models that contain fluid interfaces rely upon interface evolution models to approximate the transition to turbulence near interfaces, in the presence of Rayleigh–Taylor (RTI) or Richtmyer–Meshkov (RMI) instability. Semi-analytical models have been developed in recent decades to predict the interface growth from an initial state into the nonlinear regime. Two of these models are considered in this study. They are the Goncharov and the z-models. Both of these interface models have strengths and weaknesses, which are examined here. Both of them have been implemented in the xRAGE compressible flow solver, which models fluid interfaces. The flow solver provides the fluids acceleration as a body force to the interface model. The purpose of such interface model is to evolve the early times of interface position as a subgrid model within a compressible flow simulation in order to then initialize a turbulence model. In this work, the interface models are assessed and compared for their evolution of RTI and RMI. The z-model performed better than the Goncharov model for all cases that were explored.

42 ENGINEERING↗

DOE OSTI2022

Multiscale plasticity of geomaterials predicted via constrained optimization‐based granular micromechanics

Abstract A general framework to derive nonlinear elastic and elastoplastic material models from granular micromechanics is proposed, where a constraint‐based variational structure is introduced to classical grain contact‐based homogenization methods of hyperelasticity. Like the classical hyperelastic methods, reference solutions for closed‐form hyperelastic material models are analytically derived from the grain‐scale contact mechanics. However, unlike prior methods, the proposed homogenization framework defines closed‐form hyperelastoplastic material models that extend multiscale variational methods to granular plasticity. The proposed framework is used to develop novel granular micromechanics‐based macroscopic models for a Mises type solid, Drucker–Prager type plasticity, and grain‐contact cohesive‐debonding with a deviatorically and volumetrically coupled nonlinearly elastic response. Macroscopic plastic parameters and yield criteria are explicitly related to their microscale counterparts, for example, the friction coefficient governing intergranular slip. Numerical examples and comparison to measurements from the literature, including triaxial compaction of concrete, are provided to investigate model predictions and demonstrate calibration to experimental data.

Bryant, E. C.↗

DOE OSTI2022

Proper orthogonal decomposition based reduced-order modeling of flux-Limited gray thermal radiation

Here, in this work, a proper orthogonal decomposition (POD) based reduced-order model (ROM) is developed to solve gray, flux-limited thermal radiation diffusion. We focus on the variable opacity radiation penetration benchmark posed by Olson, Auer, and Hall. The T -3 relationship for opacity in conjunction with high-temperature radiation penetrating an initially cold material produces a strong thermal radiation shock. This class of problems is particularly challenging for standard POD-based reduced-order modeling due to the nonlinearities presented by 1) the T 4 source term, and 2) flux-limited diffusion operator. To address these challenges and develop a cost competitive ROM, we employ a “hyper-reduction” technique through discrete empirical interpolation (DEIM) and allow for adaptive reduced-order projections through principal interval decomposition (PID). Performance of the proposed methodology is quantified by comparing the cost savings and accuracy relative to a full-order computation. Reference solutions and snapshot data are obtained through a full-order calculation performed by the University of Chicago maintained astrophysics code, FLASH. For consistency and potential extensibility, the developed ROM is also implemented in FLASH. We find that in the initialization regime, where the thermal radiation wave is initially created by the warming of the material, this class of problems is highly reducible and suitable for POD-based ROMs. However, the strong convective nature of the wave propagation regime is less reducible and more challenging to create an efficient ROM.

42 ENGINEERING↗

DOE OSTI2023

Efficacy of vibro-impact energy harvesting absorbers on controlling dynamical systems under vortex-induced vibrations and base excitation

Here this study investigates improving the efficacy of an energy harvesting absorber's ability to control a structure under vortex-induced vibrations, base excitation, and a combination of the two by including mechanical amplitude stoppers. The nonlinear reduced-order model is developed through modifying trilinear spring models to represent the impact forces, a modified van der Pol oscillator to represent the forcing due to the vortex-induced vibrations and using the Euler-Lagrange principle to express the equations of motion. It is seen that a soft stopper stiffness and a 5mm gap performs the most effectively of increasing the power generated from the absorber while still greatly reducing the primary structure's amplitude. By changing the stopper's location towards the middle of the energy harvesting absorber, the large effects of the impact forces are reduced and improves the efficacy of medium and hard stopper stiffnesses to generate near the amount of power the soft stopper does, while greatly improving the control of the primary structure. When the system is under combined loadings, the large oscillations of the synchronization region cause the effective configuration to be that of a 27.5 mm gap with soft stiffnesses. The results shows that medium stiffness stoppers with small gaps generate large aperiodic regions due to the high impact force. When the oscillations are close to the stoppers, the beating phenomenon is observed and is not overpowered by the vibro-impact force.

16 TIDAL AND WAVE POWER↗

DOE OSTI2022

Local measurement of bulk thermal diffusivity using photothermal radiometry

Here, an experimental methodology using photothermal radiometry is developed for the accurate measurement of bulk thermal diffusivity of nuclear fuels and materials irradiated to high doses. Under these conditions, nuclear fuels, such as uranium oxide, and moderator materials, such as graphite, become friable, which requires characterization techniques that can accommodate irregularly shaped fragments. Photothermal radiometry, a good candidate for this application, involves locally heating a sample by using a laser and measuring the temperature field by monitoring blackbody radiation. The interaction volume for this study, less than a millimeter, is carefully chosen to sample a statistically significant number of large-scale structural features, such as pores and gas filled bubbles, and is small enough that the sample fragments can be treated as a thermal half-space. The thermal diffusivity standards considered in this study cover a range of thermal diffusivities representative of both fresh and spent nuclear fuels. We also consider a sample having a porous microstructure representative of large-scale structures found in materials irradiated to high doses. Our measurement methodology circumvents complex thermal wave models that address optical diffraction, nonlinear transfer function associated with blackbody radiation, and finite sample size effects. Consequently, the large measurement uncertainty associated with modeling these effects can be avoided. While the emphasis here is on nuclear fuels and materials, this measurement approach is well suited to measure thermal transport in a variety of technologically important materials associated with advanced synthesis techniques. Examples range from small, exotic single crystals grown using hydrothermal growth techniques to additively manufactured components having complex geometries.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Intraspecific Diversity in Thermal Performance Determines Phytoplankton Ecological Niche

ABSTRACT Temperature has a primary influence on phytoplankton physiology and ecology. We grew 12 strains of Gephyrocapsa huxleyi isolated from different‐temperature regions for ~45 generations (2 months) and characterised acclimated thermal response curves across a temperature range. Even with similar temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day −1 . Thermal niche widths varied from 16.7°C to 24.8°C, suggesting that strains use distinct thermal response mechanisms. We investigated the implications of this thermal intraspecific diversity using an ocean ecosystem simulation resolving phytoplankton thermal phenotypes. Model analogues of thermal ‘generalists’ and ‘specialists’ resulted in a distinctive global biogeography of thermal niche widths with a nonlinear latitudinal pattern. We leveraged model output to predict ranges of the 12 lab‐reared strains and demonstrated how this approach could broadly refine geographic range predictions. Our combination of observations and modelled biogeography highlights the capacity of diverse groups to survive temperature shifts.

Krinos, Arianna I. [Department of Biology Woods Ho↗

DOE OSTI2025

Transfer learning nonlinear plasma dynamic transitions in low dimensional embeddings via deep neural networks

Deep learning algorithms provide a new paradigm to study high-dimensional dynamical behaviors, such as those in fusion plasma systems. Development of novel, data-driven model reduction methods, coupled with detection of abnormal modes with plasma physics, opens a unique opportunity to identify plasma instabilities through automated construction of parsimonious models that can be tuned to balance accuracy and cost. Our fusion transfer learning (FTL) model demonstrates success in rapidly reconstructing nonlinear kink mode structures by learning from a limited amount of nonlinear simulation data. The knowledge transfer process leverages a pre-trained neural encoder–decoder network, initially trained on linear simulations, to effectively capture nonlinear dynamics. The low-dimensional embeddings extract the coherent structures of interest, while preserving the inherent dynamics of the complex system. Experimental results highlight FTL’s capacity to capture transitional behaviors and dynamical features in plasma dynamics—a task often challenging for conventional methods. The model developed in this study is generalizable and can be extended broadly through transfer learning to address various magnetohydrodynamics modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Mathematical analysis of laboratory microbial experiments demonstrating deterministic chaotic dynamics

Presented is a system of four ordinary differential equations and a mathematical analysis of microbiological experiments in a four-component chemostat—nutrient n, rods r, cocci c, and predators p. The analysis is consistent with the conclusion that previous experiments produced features of deterministic chaotic and classical dynamics depending on dilution rate. The surrogate model incorporates as much experimental detail as possible, but necessarily contains unmeasured parameters. The objective is to understand better the differences between model simulations and experimental results in complex microbial populations. The key methodology for simulation of chaotic dynamics, consistent with the measured dilution rate and microbial volume averages, was to cause the preference of p for r vs. c to vary with the r and c concentrations, to make r more competitive for nutrient than c, and to recycle some dying p biomass, leading to a modified version of the Monod kinetics model. Our mathematical model demonstrated that the occurrence of chaotic dynamics requires a predator, p, preference for r versus c to increase significantly with increases in r and c populations. Also included is a discussion of several generalizations of the existing model and a possible involvement of the minimum energy dissipation principle. This principle appears fundamental to thermodynamic systems including living systems. Several new experiments are suggested.

59 BASIC BIOLOGICAL SCIENCES↗