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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Estimating the carbon footprint of computational fluid dynamics

In this study, computational resources have grown exponentially in the past few decades. These machines make possible research and design in fields as diverse as medicine, astronomy, and engineering. Despite ever-increasing computational capabilities, direct simulation of complex systems has remained challenging owing to the degrees of freedom involved. At the cusp of exascale computing, high-resolution simulation of practical problems with minimal model assumptions may soon experience a renaissance. However, growing reliance on modern computers comes at the cost of a growing carbon footprint. To illustrate this, we examine historic computations in fluid dynamics where larger computers have afforded the opportunity to simulate flows at increasingly relevant Reynolds numbers. Under a variety of flow configurations, the carbon footprint of such simulations is found to scale roughly with the fourth power of Reynolds number. This is primarily explained by the computation cost in core-hours, which is also described by similar scaling, though regional differences in renewable energy use also play a role. Using the established correlation, we examine a large database of simulations to develop estimates for the carbon footprint of computational fluid dynamics in a given year. Collectively, the analysis provides an additional benchmark for new computations where, in addition to balancing considerations of model fidelity, carbon footprint should also be considered.

42 ENGINEERING↗
DOE OSTI2022

Stochastic Vector Techniques in Ground-State Electronic Structure

Herein we review a suite of stochastic vector computational approaches for studying the electronic structure of extended condensed matter systems. These techniques help reduce algorithmic complexity, facilitate efficient parallelization, simplify computational tasks, accelerate calculations, and diminish memory requirements. While their scope is vast, we limit our study to ground-state and finite temperature density functional theory (DFT) and second-order many-body perturbation theory. More advanced topics, such as quasiparticle (charge) and optical (neutral) excitations and higher-order processes, are covered elsewhere. We start by explaining how to use stochastic vectors in computations, characterizing the associated statistical errors. Next, we show how to estimate the electron density in DFT and discuss effective techniques to reduce statistical errors. Finally, we review the use of stochastic vectors for calculating correlation energies within the second-order Møller-Plesset perturbation theory and its finite temperature variational form. Example calculation results are presented and used to demonstrate the efficacy of the methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Advanced modeling and simulation of research reactors using dynamic mode decomposition

Full text of publication follows. Due to the ever-increasing safety requirements, the current trend of nuclear reactor analysis is shifting towards high-fidelity multi-physics models, which have a very high computational cost and modelling complexity. As the cost of even a single model run makes it impossible to analyse the behaviour and performance of these models on large-scale commercial plants, it has become even more significant to provide suitable benchmarks to validate and test them extensively. In this sense, research reactors offer a promising solution for the initial validation of high-fidelity models, as they are significantly smaller than commercial reactors and their characteristics are well known. In particular, the reactors of the TRIGA family have been used to assess and validate models and methods for Generation-IV designs, as they have some similar features (such as the dominance of natural convection as cooling mechanism and the difficulties in performing sub-channel analysis using standard codes). Still, the computational requirements of high-fidelity models make them unsuitable for real-time analysis, even following their assessment on research reactors. In this sense, Model Order Reduction (MOR) techniques give an additional strategy to reduce the computational cost of high-fidelity models (whilst preserving sufficient accuracy). In particular, this work focuses on Dynamic Mode Decomposition (DMD), a non-intrusive MOR technique that aims at representing models with explicit temporal dynamics by extracting the time-varying characteristics and the governing structures based only on a set of available data, thus without needing any underlying knowledge of the governing equations. In addition, DMD also computes a low-dimensional surrogate of the dynamic matrix of the system, making it suited for stability analysis and real-time evaluations. This work focuses on the application and validation of the DMD method on the Computational Fluid-Dynamics (CFD) model TRIGA Mark II reactor, also discussing in detail the potentiality of this algorithm as an advanced modelling tool for nuclear reactor analysis. (author)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2024

A Gaussian process based surrogate approach for the optimization of cylindrical targets

Simulating direct-drive inertial confinement experiments presents significant computational challenges, both due to the complexity of the codes required for such simulations and the substantial computational expense associated with target design studies. Machine learning models, and in particular, surrogate models, offer a solution by replacing simulation results with a simplified approximation. In this study, we apply surrogate modeling and optimization techniques that are well established in the existing literature to one-dimensional simulation data of a new cylindrical target design containing deuterium–tritium fuel. These models predict yields without the need for expensive simulations. We find that Bayesian optimization with Gaussian process surrogates enhances sampling efficiency in low-dimensional design spaces but becomes less efficient as dimensionality increases. Nonetheless, optimization routines within two-dimensional and five-dimensional design spaces can identify designs that maximize yield, while also aligning with established physical intuition. Optimization routines, which ignore constraints on hydrodynamic instability growth, are shown to lead to unstable designs in 2D, resulting in yield loss. However, routines that utilize 1D simulations and impose constraints on the in-flight aspect ratio converge on novel cylindrical target designs that are stable against hydrodynamic instability growth in 2D and achieve high yield.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2024

Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition

Abstract Vibrational spectroscopy allows us to understand complex physical and chemical interactions of molecular crystals and liquids such as ammonia, which has recently emerged as a strong hydrogen fuel candidate to support a sustainable society. We report inelastic neutron scattering measurement of vibrational properties of ammonia along the solid-to-liquid phase transition with high enough resolution for direct comparisons to ab-initio simulations. Theoretical analysis reveals the essential role of nuclear quantum effects (NQEs) for correctly describing the intermolecular spectrum as well as high energy intramolecular N-H stretching modes. This is achieved by training neural network models using ab-initio path-integral molecular dynamics (PIMD) simulations, thereby encompassing large spatiotemporal trajectories required to resolve low energy dynamics while retaining NQEs. Our results not only establish the role of NQEs in ammonia but also provide general computational frameworks to study complex molecular systems with NQEs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Reduced salen in a monomeric Fe complex

We report the first monomeric formally M I transition metal salen complex without ion pairing. A combination of spectroscopy, crystallography, and computations indicates that reduction of an Fe II salen complex gives substantial reduced ligand character. We also present a computational method for accurately predicting 57 Fe Mössbauer parameters of Fe salen complexes.

Feldman, Dana M. [Yale University, New Haven, CT (↗
DOE OSTI2025

Parameterized anomalous transport model for current-carrying collisionless plasmas in pulsed power inertial confinement fusion

Current delivery in pulsed power inertial confinement fusion is influenced by collisionless current-carrying microturbulent plasmas, which are sourced from electrode surfaces. In this setting, the lower hybrid drift instability—triggered by plasma acceleration—is a leading candidate driver of difficult-to-predict momentum and energy transport. To characterize the nonlinear state of the microturbulent plasma, a parameterized anomalous transport model is developed for the instability, with analytic formulas for anomalous collision frequency, resistivity, and species heating rates. The formulas are expressed in terms of linear-theory variables and four dimensionless parameters that characterize the macroscopic plasma state. The model is built on linear theory analysis, power law analysis, and quasilinear theory analysis, and is validated using a series of nonlinear continuum kinetic Vlasov–Poisson simulations. The theoretical and computational investigation demonstrates that the anomalous collision frequency associated with the instability can be reliably approximated, within about a factor of five or better, by the unscaled linear theory growth rate of the fastest-growing wavenumber mode. This finding enables efficient calculation of anomalous resistivity and species heating rates over a wide range of plasma conditions, resulting in improved predictive capabilities.

Complex functions↗
DOE OSTI2022

Model reduction methods for nuclear emulators

The field of model order reduction (MOR) is growing in importance due to its ability to extract the key insights from complex simulations while discarding computationally burdensome and superfluous information. We provide an overview of MOR methods for the creation of fast & accurate emulators of memory- and compute-intensive nuclear systems, focusing on eigen-emulators and variational emulators. As an example, we describe how 'eigenvector continuation' is a special case of a much more general and well-studied MOR formalism for parameterized systems. We continue with an introduction to the Ritz and Galerkin projection methods that underpin many such emulators, while pointing to the relevant MOR theory and its successful applications along the way. Here, we believe that this guide will open the door to broader applications in nuclear physics and facilitate communication with practitioners in other fields.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel

We report despite the progress in modeling complex molecular systems of ever-increasing complexity, a quantitatively accurate computational treatment of ion permeation through narrow membrane channels remains challenging. An important factor to reach this goal is induced electronic polarization, which is likely to impact the permeation rate of small ions through narrow molecular pores. In this work, we extended the recently developed polarizable force field based on the classical Drude oscillators to assess the role of induced polarization effects on the energetics of sodium and potassium ion transport across the gramicidin A (gA) ion channel. The inclusion of induced polarization lowers barriers present in 1D potential of mean force (PMF) for cation permeation by ~50% compared to those obtained with the additive force field. Conductance properties calculated with 1D PMFs from Drude simulations are in better agreement with experimental results. Polarization of single-file water molecules and protein atoms forming the narrow pore has a direct impact on the free-energy barriers and cation-specific solid-state NMR chemical shifts. Sensitivity analysis indicates that small changes to water–channel interactions can alter the free energy barrier for ion permeation. These results, illustrating polarization effects present in the complex electrostatic environment of the gA channel, have broad implications for revising proposed mechanisms of ion permeation and selectivity in a variety of ion channels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Sparse Approximate Multifrontal Factorization with Butterfly Compression for High-Frequency Wave Equations

In this work, we present a fast and approximate multifrontal solver for large-scale sparse linear systems arising from finite-difference, finite-volume or finite-element discretization of high-frequency wave equations. The proposed solver leverages the butterfly algorithm and its hierarchical matrix extension for compressing and factorizing large frontal matrices via graph-distance guided entry evaluation or randomized matrix-vector multiplication-based schemes. Complexity analysis and numerical experiments demonstrate $\mathcal{O}(N\log^2 N)$ computation and $\mathcal{O}(N)$ memory complexity when applied to an $N\times N$ sparse system arising from 3D high-frequency Helmholtz and Maxwell problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Quantifying the generalization error in deep learning in terms of data distribution and neural network smoothness

We report the accuracy of deep learning, i.e., deep neural networks, can be characterized by dividing the total error into three main types: approximation error, optimization error, and generalization error. Whereas there are some satisfactory answers to the problems of approximation and optimization, much less is known about the theory of generalization. Most existing theoretical works for generalization fail to explain the performance of neural networks in practice. To derive a meaningful bound, we study the generalization error of neural networks for classification problems in terms of data distribution and neural network smoothness. We introduce the cover complexity (CC) to measure the difficulty of learning a data set and the inverse of the modulus of continuity to quantify neural network smoothness. A quantitative bound for expected accuracy/error is derived by considering both the CC and neural network smoothness. Although most of the analysis is general and not specific to neural networks, we validate our theoretical assumptions and results numerically for neural networks by several data sets of images. The numerical results confirm that the expected error of trained networks scaled with the square root of the number of classes has a linear relationship with respect to the CC. We also observe a clear consistency between test loss and neural network smoothness during the training process. In addition, we demonstrate empirically that the neural network smoothness decreases when the network size increases whereas the smoothness is insensitive to training dataset size.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Dislocation Patterning in Deforming Crystals: Theory, Computational Predictions and Validation (Final Technical Report)

This project was awarded for an initial period of three years, followed by a no-cost extension for one year and a funded one-year renewal. During the first four years, the project focused on investigating the role of dislocation reactions and dislocation correlation in dislocation patterning in FCC metals. During the fifth year, the scope of research was expanded to investigate the effects of composition inhomogeneity on the mesoscale plastic response of Body-Centered Cubic (BCC) alloys. In addition to its impact on metal hardening during deformation, dislocation patterning provides the microstructure information required to understand phenomena like fracture and recrystallization in metals. The Continuum Dislocation Dynamics (CDD) framework was the methodology used during the first four years, followed by the use of Discrete Dislocation Dynamics (DDD) during the fifth year. CDD is a density-based formalism of dislocation dynamics in which the plastic deformation of crystals is predicted together with the mesoscale dislocation patterns by tracking the space-time evolution of dislocations as driven by the applied stress, short-range and long-range interactions of dislocations, and cross slip. CDD is a crystal mechanics approach in which the plastic constitutive part is replaced with the equations of dislocation dynamics, which is driven by the internal stress via a mobility laws, while the evolution of the density gives the eigenstrain required to update the internal stress itself. The governing equations are thus those of crystal mechanics cast as an eigenstrain problem and those of dislocation transport and reactions. Our investigations during the first four years were driven by the hypothesis that that dislocation patterning is triggered by spatiotemporal dislocation density and internal stress fluctuations, and that such fluctuations influence the collective dislocation dynamic through their effects on the short-range reaction rates and the collective dislocation mobility. This hypothesis was tested by modeling the influence of the dislocation reactions and dislocation correlations on collective dislocation dynamics. The main research components during the first four years were: 1) Reformulation of the CDD framework to integrate the dislocation correlations and dislocation reactions. 2) Simulation of the dislocation correlations and quantifying their contribution to the long-range stress of complex dislocation systems. 3) Computational implementation of the updated CDD model for FCC single crystals and development of an efficient CDD code. 4) Investigation of dislocation patterning in FCC crystals based on the updated CDD model. Some key findings from these investigations were: 1) The patterning of dislocations is initiated by cross slip and internal stress fluctuations, and the refinement of the pattern results from junction formation. 2) Patterning is more prominent under high stress. 3) The correlation stress was found to be a significant part of the mean field stress in continuum representations of dislocation dynamics. During the last year of the project, we have established a method for performing dislocation dynamics in inhomogeneous alloys and demonstrated the impact of composition inhomogeneity on the characteristics of initial yielding and dislocation character in BCC alloys. We also tested this method using an irradiated ferritic alloy in which the composition and dislocation loops effects are both present. In doing so, we have considered two aspects of the role of inhomogeneity, the creation of internal coherency stress due to the dependence of the lattice parameter on the local composition, and the dependence of the dislocation mobility on the local composition. These two aspects resulted in an unexpected behavior of the dislocation system, and, in turn, the yielding behavior of BCC alloys. Key findings include: 1) The composition inhomogeneity in BCC alloys alters the well-known role of screw dislocations by forcing a level of waviness on the average dislocation character, thus destroying the screw character dominance in the yielding observed in pure or homogeneous BCC metals. 2) In the case of irradiated alloys, while composition inhomogeneity by itself and dislocation loops by themselves result in some hardening, the superposition of the two mechanisms does not result in the sum of the two contributions via any known rule. The latter result contradicts the classical works related hardening via multiple mechanisms, which state that various hardening mechanisms can be added linearly or using some Pythagorean additive rule. We were able to rationalize this unexpected result by a closer loop at the origin of the hardening mechanisms themselves, which both involved long-range elastic interactions with dislocations. We reached the conclusion that the hardening resulting from the total stress associated with these two mechanisms (current work) differs from the sum of the effects of the individual stress fields (classical literature). We have also found a major flaw in the classical theory of spinodal hardening. The latter theory never considered the impact of composition undulation on the solute hardening. We have built a new general theory accounting for the effect of solute friction together with the composition undulations on the dislocation configuration at Critical Resolved Shear Stress (CRSS), which is yielding a new definition of the spinodal hardening and new different results. This work is the first to recognize the lack of the role of solute in spinodal hardening theory of alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Leveraging Machine Learning Capabilities for the Characterization of Irradiated Uranium: A Case Study of Analysis Methods for Nuclear Safeguards and Nuclear Forensics

Nondestructively determining the initial enrichment of irradiated uranium is a complex and laborious multivariable problem due to the presence of fission products. This work demonstrates the capabilities of machine learning to analyze gamma-ray spectral data to determine initial enrichment without knowledge of the decay time of the sample. The approach developed is agnostic to the particular scenario and is applicable to a wide variety of applications in nuclear forensics and nuclear safeguards. We irradiated 5 mg uranium standard reference materials at discrete enrichment values ranging from 0.02% to 97% 235 U (weight percent) in UT Austin’s Nuclear Engineering Teaching Laboratory TRIGA Mark II 1.1 MW research reactor, allowed each to decay for 8 hours, and then measured each sample via gamma-ray spectrometry for 50 hours post-irradiation yielding 1,400 individual gamma-ray spectra discretized into 8,192 energy bins. We then trained decision trees models to analyze individual gamma-ray spectra and estimate the associated initial enrichment without knowledge of the time since end of irradiation. We evaluated the performance of the models with a reserved test set not used for training or calibrating the model. A decision tree model constructed with this procedure achieved a mean absolute error in initial enrichment determination of 2.3% (weight percent 235 U). Next, we implemented a principal component analysis pre-processing routine of the gamma-ray spectrometry data to reduce the dimensionality of the dataset from 8,192 channels in the spectrum to 10 principal components while retaining over 99% of the inherent variance in the data. Decision tree models constructed with these data demonstrated decreased mean absolute error in enrichment determination, reduced computational time, and decreased complexity. A single decision tree model constructed with this procedure achieved a mean absolute error in initial enrichment determination of 0.05% (weight percent 235 U). Furthermore, we analyzed these models with learning curves to ensure that overfitting did not occur. The capabilities provided by these models can be naturally extended to other application-focused measurements in the fields of nuclear safeguards, nuclear forensics, and nuclear non-proliferation.

Drescher, Adam↗
DOE OSTI2022

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

Computational approaches for predicting protein-protein interfaces are extremely useful for understanding and modelling the quaternary structure of protein assemblies. In particular, partner-specific binding site prediction methods allow delineating the specific residues that compose the interface of protein complexes. In recent years, new machine learning and other algorithmic approaches have been proposed to solve this problem. However, little effort has been made in finding better training datasets to improve the performance of these methods. With the aim of vindicating the importance of the training set compilation procedure, in this work we present BIPSPI+, a new version of our original server trained on carefully curated datasets that outperforms our original predictor. We show how prediction performance can be improved by selecting specific datasets that better describe particular types of protein interactions and interfaces (e.g. homo/hetero). In addition, our upgraded web server offers a new set of functionalities such as the sequence-structure prediction mode, hetero- or homo-complex specialization and the guided docking tool that allows to compute 3D quaternary structure poses using the predicted interfaces. BIPSPI+ is freely available at https://bipspi.cnb.csic.es.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Bayesian Approach for Quantifying Data Scarcity when Modeling Human Behavior via Inverse Reinforcement Learning

Computational models that formalize complex human behaviors enable study and understanding of such behaviors. However, collecting behavior data required to estimate the parameters of such models is often tedious and resource intensive. Thus, estimating dataset size as part of data collection planning (also known as Sample Size Determination) is important to reduce the time and effort of behavior data collection while maintaining an accurate estimate of model parameters. In this paper, we present a sample size determination method based on Uncertainty Quantification (UQ) for a specific Inverse Reinforcement Learning (IRL) model of human behavior, in two cases: 1) pre-hoc experiment design—conducted in the planning stage before any data is collected, to guide the estimation of how many samples to collect; and 2) post-hoc dataset analysis—performed after data is collected, to decide if the existing dataset has sufficient samples and whether more data is needed. Here, we validate our approach in experiments with a realistic model of behaviors of people with Multiple Sclerosis (MS) and illustrate how to pick a reasonable sample size target. Our work enables model designers to perform a deeper, principled investigation of effects of dataset size on IRL.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Time Series Dimension Reduction for Surrogate Models of Port Scanning Cyber Emulations

Surrogate model development is a key resource in the scientific modeling community for providing computational expedience when simulating complex systems without loss of great fidelity. The initial step to development of a surrogate model is identification of the primary governing components of the system. Principal component analysis (PCA) is a widely used data science technique that provides inspection of such driving factors, when the objective for modeling is to capture the greatest sources of variance inherent to a dataset. Although an efficient linear dimension reduction tool, PCA makes the fundamental assumption that the data is continuous and normally distributed. Thus, it provides ideal performance when these conditions are met. In the case for which cyber emulations provide realizations of a port scanning scenario, the data to be modeled follows a discrete time series function comprised of monotonically increasing piece-wise constant steps. The sources of variance are related to the timing and magnitude of these steps. Therefore, we consider using XPCA, an extension to PCA for continuous and discrete random variates. This report provides the documentation of the trade-offs between the PCA and XPCA linear dimension reduction algorithms, for the intended purpose to identify key components of greatest variance in our time series data. These components will ultimately provide the basis for future surrogate models of port scanning cyber emulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Mixed-mode oscillations in a three-timescale coupled Morris–Lecar system

Mixed-mode oscillations (MMOs) are complex oscillatory behaviors of multiple-timescale dynamical systems in which there is an alternation of large-amplitude and small-amplitude oscillations. It is well known that MMOs in two-timescale systems can arise either from a canard mechanism associated with folded node singularities or a delayed Andronov–Hopf bifurcation (DHB) of the fast subsystem. While MMOs in two-timescale systems have been extensively studied, less is known regarding MMOs emerging in three-timescale systems. In this work, we examine the mechanisms of MMOs in coupled Morris–Lecar neurons with three distinct timescales. We investigate two kinds of MMOs occurring in the presence of a singularity known as canard-delayed-Hopf (CDH) and in cases where CDH is absent. In both cases, we examine how features and mechanisms of MMOs vary with respect to variations in timescales. Our analysis reveals that MMOs supported by CDH demonstrate significantly stronger robustness than those in its absence. Moreover, we show that the mere presence of CDH does not guarantee the occurrence of MMOs. This work yields important insights into conditions under which the two separate mechanisms in two-timescale context, canard and DHB, can interact in a three-timescale setting and produce more robust MMOs, particularly against timescale variations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

How generic is iodide-tagging photoelectron spectroscopy: An extended investigation on the Gly· X - (Gly = glycine, X = Cl or Br) complexes

We report a joint negative ion photoelectron spectroscopy (NIPES) and quantum chemical computational study on glycine-chloride/bromide complexes (denoted Gly·X - , X = Cl/Br) in close comparison to the previously studied Gly·I - cluster ion. Combining experimental NIPE spectra and theoretical calculations, various Gly·X - complexes were found to adopt the same types of low-lying isomers, albeit with different relative energies. Despite more congested spectral profiles for Gly·Cl - and Gly·Br - , spectral assignments were accomplished with the guidance of the knowledge learned from Gly·I - , where a larger spin–orbit splitting of iodine afforded well-resolved, recognizable spectral peaks. Three canonical plus one zwitterionic isomer for Gly·Cl - and four canonical conformers for Gly·Br - were experimentally identified and characterized in contrast to the five canonical ones observed for Gly·I - under similar experimental conditions. Taken together, this study investigates both genericity and variations in binding patterns for the complexes composed of glycine and various halides, demonstrating that iodide-tagging is an effective spectroscopic means to unravel diverse ion-molecule binding motifs for cluster anions with congested spectral bands by substituting the respective ion with iodide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗