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At least 469 records · Page 26

Self-consistent formation of parallel electric fields in the auroral zone

This paper presents results from a fully self-consistent kinetic particle simulation of the time-dependent formation of large scale parallel electric fields in the auroral zone. The results show that magnetic mirroring of the hot plasma that streams earthward from the magnetotail leads to a charge separation potential drop of many kilovolts, over an altitude range of a few thousand kilometers. Once the potential drop is formed, it remains relatively static and is maintained in time by the constant input of hot plasma from the tail; the parallel electric field accelerates ions away from Earth and ionospheric electrons towards the Earth. At altitudes above where the ions are mirror reflected and accelerated by the parallel electric field, low frequency waves are generated, possibly due to an ion/ion two-stream interaction.

Schriver, David↗

Toward active disruption avoidance via real-time estimation of the safe operating region and disruption proximity in tokamaks

This paper describes a real-time capable algorithm for identifying the safe operating region around a tokamak operating point. The region is defined by a convex set of linear constraints, from which the distance of a point from a disruptive boundary can be calculated. The disruptivity of points is calculated from an empirical machine learning predictor that generates the likelihood of disruption. While the likelihood generated by such empirical models can be compared to a threshold to trigger a disruption mitigation system, the safe operating region calculation enables active optimization of the operating point to maintain a safe margin from disruptive boundaries. The proposed algorithm is tested using a random forest disruption predictor fit on data from DIII-D. The safe operating region identification algorithm is applied to historical data from DIII-D showing the evolution of disruptive boundaries and the potential impact of optimization of the operating point. Real-time relevant execution times are made possible by parallelizing many of the calculation steps and implementing the algorithm on a graphics processing unit. Lastly, a real-time capable algorithm for optimizing the target operating point within the identified constraints is also proposed and simulated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

OpenMP Parallelization and Optimization of Graph-Based Machine Learning Algorithms

In this paper, we investigate the OpenMP parallelization and optimization of two novel data classification algorithms. The new algorithms are based on graph and PDE solution techniques and provide significant accuracy and performance advantages over traditional data classification algorithms in serial mode. The methods leverage the Nystrom extension to calculate eigenvalue/eigenvectors of the graph Laplacian and this is a self-contained module that can be used in conjunction with other graph-Laplacian based methods such as spectral clustering. We use performance tools to collect the hotspots and memory access of the serial codes and use OpenMP as the parallelization language to parallelize the most time-consuming parts. Where possible, we also use library routines. We then optimize the OpenMP implementations and detail the performance on traditional supercomputer nodes (in our case a Cray XC30), and test the optimization steps on emerging testbed systems based on Intel’s Knights Corner and Landing processors. We show both performance improvement and strong scaling behavior. Finally, a large number of optimization techniques and analyses are necessary before the algorithm reaches almost ideal scaling.

97 MATHEMATICS AND COMPUTING↗

Randomized Preconditioned Solvers for Strong Constraint 4D-Var Data Assimilation

The Strong Constraint 4D Variational (SC-4DVAR) data assimilation method is widely used in climate and weather applications. SC-4DVAR involves solving a minimization problem to compute the maximum a posteriori estimate, which we tackle using the Gauss-Newton method. The computation of the descent direction is expensive since it involves the solution of a large-scale and potentially ill-conditioned linear system, solved using the preconditioned conjugate gradient (PCG) method. Here, to address this cost, we efficiently construct scalable preconditioners using three different randomization techniques, which all rely on a certain low-rank structure involving the Gauss-Newton Hessian. The proposed techniques come with theoretical guarantees on the condition number, and at the same time, are amenable to parallelization. We also develop an adaptive approach to estimate the sketch size and choose between the reuse or recomputation of the preconditioner. We demonstrate the performance and effectiveness of our methodology on two representative model problems—the Burgers and barotropic vorticity equation—showing a drastic reduction in both the number of PCG iterations and the number of Gauss-Newton Hessian products after including the preconditioner construction cost.

Gauss-Newton↗

Shifting modes of iron sulfidization at the onset of OAE-2 drive regional shifts in pyrite δ 34 S records

We report total reduced inorganic S isotope ratios (δ 34 S CRS ) shift toward more negative values across much of the southern North Atlantic just before the onset of the Cenomanian-Turonian Ocean Anoxic Event (OAE-2). At the same time, there is no parallel isotopic change in the significantly larger pool of kerogen (organic) S, which indicates that the distribution and S-isotope composition of sulfide in the environment likely did not drive the change in δ 34 S CRS . Here, we investigate possible explanations for the negative shift in δ 34 S CRS values and their divergence from organic S by isolating iron sulfides for morphological identification and grain-specific isotopic analysis using secondary ion mass spectrometry (SIMS). In pre- and syn-OAE-2 sedimentary rocks from Demerara Rise, we find four distinct morphologies of iron sulfides: pyrite framboids (1–20 μm diameter), irregular pyrite aggregates (1–38 μm diameter), large cemented pyrite aggregates (~60 μm diameter), and irregular and cemented aggregates of the pyrite polymorph marcasite (1–45 μm diameter). These different textural groups have distinct S-isotopic compositions that are largely consistent through the onset of OAE-2. As such, the secular change in bulk δ 34 S CRS values likely reflects the changing proportions of these phases stratigraphically across OAE-2. All textural groups feature resolvable intra-grain δ 34 S variability, suggesting that the environments in which they formed were characterized by dynamic sulfide δ 34 S values and/or by partial closed-system distillation. We use grain-specific δ 34 S distributions to rule out shoaling of the chemocline within the sediments as a mechanism for the observed decrease in δ 34 S CRS . Instead, we propose that changes in the reactivity of the iron species delivered to Demerara Rise over the ~200 kyr leading up to the onset of OAE-2 impacted the relative contributions of pyrite with S-isotope signatures reflecting the water column, shallow sediments, and deeper sediments to the bulk sedimentary δ 34 S CRS value. Specifically, the change in iron reactivity at the onset of OAE-2 favored the production of 34 S-depleted large, cemented aggregates and framboids at the expense of more 34 S-enriched irregular aggregates. Our results underscore that bulk δ 34 S CRS measurements integrate multiple reduced phases that form via distinct reaction mechanisms and potentially in different parts of the depositional environment. Grain-specific SIMS analyses dramatically enrich our ability to interpret pyrite isotopic patterns in the geologic record.

58 GEOSCIENCES↗

Sparse, iterative simulation methods for one-dimensional laminar flames

Sparse, iterative simulation methods for one-dimensional laminar flames are proposed. The resulting steady and unsteady flame solvers exploit approximate Jacobians to greatly reduce the computational cost associated with matrix operations. The constant, non-unity Lewis number assumption is introduced to further reduce the computational cost. The solvers are also parallelized to reduce time-to-solution on distributed memory computer systems. Computed laminar flame speeds and species profiles for a range of chemical mechanisms (from 10 to 2878 species) are compared against a well-validated commercial code and are found to be consistent within solver tolerances. The computation times of both the unsteady and steady solutions increase only linearly with the number of species, which is a significant improvement over the quadratic or cubic scaling of existing steady-state flame solvers. For the largest mechanism tested, the steady-state flame solver is two orders of magnitude faster than commonly-used codes. The use of an approximate Jacobian is shown to reduce the rate of convergence for the steady-state solver, but does not significantly affect the domain of convergence. The steady-state solver with approximate Jacobian is thus well suited for computationally efficient laminar flame speed sweeps with large kinetic mechanisms.

42 ENGINEERING↗

Advancing specialized biofoundries via automated adaptive laboratory evolution

Adaptive laboratory evolution (ALE) is a powerful strategy for improving microbial phenotypes by harnessing natural selection under defined environmental conditions. Through applying selection regimes, beneficial mutations accumulate, enabling the generation of strains with enhanced properties. However, conventional ALE is labor-intensive and difficult to scale, limiting reproducibility and broader discovery of evolutionary principles. Recent advances in robotics, automation, and computational infrastructure are transforming ALE into a scalable, data-rich experimental paradigm. Automated platforms enable standardized and complex protocols, real-time monitoring, and highly parallel evolution campaigns, improving consistency while generating longitudinal datasets that reveal convergent adaptive mechanisms. Here, we discuss the role of specialized biofoundries in advancing automated ALE and enabling large-scale evolutionary engineering. We review major automated ALE formats and outline key design principles for effective ALE biofoundries, highlighting how automated ALE can support autonomous experimentation and AI-guided strain engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Domain decomposition in time for PDE-constrained optimization

Here, PDE-constrained optimization problems have a wide range of applications, but they lead to very large and ill-conditioned linear systems, especially if the problems are time dependent. In this paper we outline an approach for dealing with such problems by decomposing them in time and applying an additive Schwarz preconditioner in time, so that we can take advantage of parallel computers to deal with the very large linear systems. We then illustrate the performance of our method on a variety of problems.

97 MATHEMATICS AND COMPUTING↗

Finite-difference schemes for anisotropic diffusion

In fusion plasmas diffusion tensors are extremely anisotropic due to the high temperature and large magnetic field strength. This causes diffusion, heat conduction, and viscous momentum loss, to effectively be aligned with the magnetic field lines. This alignment leads to different values for the respective diffusive coefficients in the magnetic field direction and in the perpendicular direction, to the extent that heat diffusion coefficients can be up to 10{sup 12} times larger in the parallel direction than in the perpendicular direction. This anisotropy puts stringent requirements on the numerical methods used to approximate the MHD-equations since any misalignment of the grid may cause the perpendicular diffusion to be polluted by the numerical error in approximating the parallel diffusion. Currently the common approach is to apply magnetic field-aligned coordinates, an approach that automatically takes care of the directionality of the diffusive coefficients. This approach runs into problems at x-points and at points where there is magnetic re-connection, since this causes local non-alignment. It is therefore useful to consider numerical schemes that are tolerant to the misalignment of the grid with the magnetic field lines, both to improve existing methods and to help open the possibility of applying regular non-aligned grids. To investigate this, in this paper several discretization schemes are developed and applied to the anisotropic heat diffusion equation on a non-aligned grid.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Two-fluid and kinetic transport physics of Kelvin–Helmholtz instabilities in nonuniform low-beta plasmas

Hall-magnetohydrodynamic (Hall-MHD) theory, two-fluid simulations, and kinetic simulations are used in this work to investigate the cross-field transport properties of Kelvin–Helmholtz instabilities in nonuniform low-beta collisionless plasmas. Hall-MHD analysis shows how the linear properties of the instability are modified by density gradients and magnetization. High-order accurate two-fluid and kinetic simulations, with complete dynamics of finite-mass electrons and ions, are applied to a suite of parameter cases to systematically assess the effects of diamagnetic drift, magnetization, charge separation, and finite Larmor motion. Initialization of exact two-species kinetic equilibria facilitates the study of isolated physical effects and enables detailed cross-comparisons between two-fluid and kinetic simulations, including for cases where ion gyroradii are comparable to gradient scale lengths. For nonuniform plasmas with significant space charge, the results of two-fluid and kinetic simulations are found to disagree with Hall-MHD predictions. Kelvin–Helmholtz instability growth rates, per unit shear, are shown to be smaller when ion diamagnetic drift and $E \times B$ drift are parallel and larger when the two drifts are antiparallel. The effect is attributed to polarization drift in the shear layer, which leads to redistribution of charge, alters the electric field that drives plasma advection, and consequently modifies growth rates. Instability-induced mass transport for different parameters is characterized in terms of the flux across the shear layer and a simplified diffusion model. Distribution functions from kinetic simulations are shown to deviate substantially from Maxwellian reconstructions, indicating the importance of kinetic physics during the nonlinear phase of the instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A resistive MHD model and simulation on plasma flow evolution in the presence of resonant magnetic perturbation in a tokamak

Nonaxisymmetric magnetic fields such as the intrinsic error field and the externally applied resonant magnetic perturbation (RMP) in a tokamak are known to influence the plasma momentum transport and flow evolution through plasma response, which itself strongly depends on the plasma flow as well. The nonlinear interaction between plasma response and flow has been previously modeled in the conventional error field theory with the “no-slip” condition, which has been recently extended to allow the “free-slip” condition. In this work, we further target this specific process and numerically simulate the nonlinear plasma response and flow evolution in the presence of a single-helicity RMP in a circular-shaped model tokamak configuration, based on the full resistive MHD model in the initial-value code NIMROD. Time evolution of the parallel (to k) flow or “slip frequency” profile and its asymptotic steady state obtained from the NIMROD simulations are compared with both conventional and extended nonlinear response theories. Here, k is the wave vector of the propagating island. Good agreement with the extended theory with free-slip condition has been achieved for the parallel flow profile evolution in response to RMP in all resistive regimes, whereas the difference from the conventional theory with the no-slip condition tends to diminish as the plasma resistivity approaches zero.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ANALYTIC FORMS OF THE PERPENDICULAR DIFFUSION COEFFICIENT IN NRMHD TURBULENCE

In the past different analytic limits for the perpendicular diffusion coefficient of energetic particles interacting with magnetic turbulence were discussed. These different limits or cases correspond to different transport modes describing how the particles are diffusing across the large-scale magnetic field. In the current paper we describe a new transport regime by considering the model of noisy reduced magnetohydrodynamic turbulence. We derive different analytic forms of the perpendicular diffusion coefficient, and while we do this, we focus on the aforementioned new transport mode. We show that for this turbulence model a small perpendicular diffusion coefficient can be obtained so that the latter diffusion coefficient is more than hundred times smaller than the parallel diffusion coefficient. This result is relevant to explain observations in the solar system where such small perpendicular diffusion coefficients have been reported.

79 ASTRONOMY AND ASTROPHYSICS↗

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗

ANISOTROPIC INTERMITTENCY OF MAGNETOHYDRODYNAMIC TURBULENCE

A higher-order multiscale analysis of spatial anisotropy in inertial range magnetohydrodynamic turbulence is presented using measurements from the STEREO spacecraft in fast ambient solar wind. We show for the first time that, when measuring parallel to the local magnetic field direction, the full statistical signature of the magnetic and Elsässer field fluctuations is that of a non-Gaussian globally scale-invariant process. This is distinct from the classic multiexponent statistics observed when the local magnetic field is perpendicular to the flow direction. These observations are interpreted as evidence for the weakness, or absence, of a parallel magnetofluid turbulence energy cascade. As such, these results present strong observational constraints on the statistical nature of intermittency in turbulent plasmas.

79 ASTRONOMY AND ASTROPHYSICS↗

Multilevel Parareal Algorithm with Averaging for Oscillatory Problems

The present study is an extension of the work done by Peddle, Haut, and Wingate and Haut and Wingate, where a two-level Parareal method with mapping and averaging is examined. The method proposed in this paper is a multilevel Parareal method with arbitrarily many levels, which is not restricted to the two-level case. We give an asymptotic error estimate which reduces to the two-level estimate for the case when only two levels are considered. Introducing more than two levels has important consequences for the averaging procedure, as we choose separate averaging windows for each of the different levels, which is an additional new feature of the present study. The different averaging windows make the proposed method especially appropriate for nonlinear multiscale problems, because we can introduce a level for each intrinsic scale of the problem and adapt the averaging procedure such that we reproduce the behavior of the model on the particular scale resolved by the level. The method is applied to nonlinear differential equations. The nonlinearities can generate a range of frequencies in the problem. The computational cost of the new method is investigated and studied on several examples.

97 MATHEMATICS AND COMPUTING↗

Dictionary Learning with Accumulator Neurons

The Locally Competitive Algorithm (LCA) uses local competition between non-spiking leaky integrator neurons to infer sparse representations, allowing for potentially real-time execution on massively parallel neuromorphic architectures such as Intel's Loihi processor. Here, we focus on the problem of inferring sparse representations from streaming video using dictionaries of spatiotemporal features optimized in an unsupervised manner for sparse reconstruction. Non-spiking LCA has previously been used to achieve unsupervised learning of spatiotemporal dictionaries composed of convolutional kernels from raw, unlabeled video. We demonstrate how unsupervised dictionary learning with spiking LCA (\hbox{S-LCA}) can be efficiently implemented using accumulator neurons, which combine a conventional leaky-integrate-and-fire (\hbox{LIF}) spike generator with an additional state variable that is used to minimize the difference between the integrated input and the spiking output. We demonstrate dictionary learning across a wide range of dynamical regimes, from graded to intermittent spiking, for inferring sparse representations of both static images drawn from the CIFAR database as well as video frames captured from a DVS camera. On a classification task that requires identification of the suite from a deck of cards being rapidly flipped through as viewed by a DVS camera, we find essentially no degradation in performance as the LCA model used to infer sparse spatiotemporal representations migrates from graded to spiking. We conclude that accumulator neurons are likely to provide a powerful enabling component of future neuromorphic hardware for implementing online unsupervised learning of spatiotemporal dictionaries optimized for sparse reconstruction of streaming video from event based DVS cameras.

artificial intelligence↗

Final Report on Project “Ton-scale Germanium: Beyond Zeptobarn WIMP Cross-section”

The DOE CAREER proposal primarily focused on establishing a modern semiconductor detector fabrication facility that would provide significant improvement in the cost profile and performance of the cryogenic semiconductor detectors used by the CDMS experiment so as to enable a next generation ton-scale experiment. The proposal also included significant work on performing data analysis on the Soudan experiment.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Computation Annual Report (2013)

Computation provides the intellectual electricity that helps make Lawrence Livermore National Laboratory (LLNL) a thriving and innovative research and development (R&D) institution. Our hardware, software, and discipline experts are integrated into almost every field of research at LLNL. Our in-house programs, software applications, and support initiatives help achieve mission-critical national-security objectives for the U.S. Departments of Energy, Homeland Security, and Defense, as well as other federal and state agencies. We deliver comprehensive support to a wide set of scientific disciplines that include physical sciences (materials modeling, fluid dynamics), biology (genomic sequencing), mathematics (scalable algorithms), and computer sciences (parallel processing, real-time control systems). This year, we have expanded our outreach with high performance computing (HPC) collaborations and made great strides in our capabilities related to mathematical computation, control systems, and computation infrastructure, many of them in concert with partners in industry and academia. The Computation workforce remains highly motivated and passionate about melding computational expertise with cutting-edge science and technology to enable breakthroughs. 2013 has once again proven that Computation provides the foundation and support that are essential for productivity at LLNL. Every scientific discipline and program leverages the tools and expertise provided by our staff. We remain at the forefront of HPC moving towards exascale and have developed the infrastructure and proficiency to make this an achievable goal. Our researchers repeatedly deliver outstanding research, attracting collaborations with the biggest names in academia and industry, while joining forces with other national laboratories to further push the bounds of what is scientifically possible. Computation’s mission is echoed by the President of the United States in his assertion that “our future depends on reaffirming America’s role as the world’s engine of scientific discovery and technological innovation.” Driven by this lofty goal, we employ our state-of-the-art computational capabilities to ensure LLNL’s position as a global science and technology leader.

97 MATHEMATICS AND COMPUTING↗