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At least 145 records · Page 8

An adaptive scalable fully implicit algorithm based on stabilized finite element for reduced visco-resistive MHD

The magnetohydrodynamics (MHD) equations are continuum models used in the study of a wide range of plasma physics systems, including the evolution of complex plasma dynamics in tokamak disruptions. However, efficient numerical solution methods for MHD are extremely challenging due to disparate time and length scales, strong hyperbolic phenomena, and nonlinearity. Additionally, therefore the development of scalable, implicit MHD algorithms and high-resolution adaptive mesh refinement strategies is of considerable importance. In this work, we develop a high-order stabilized finite-element algorithm for the reduced visco-resistive MHD equations based on the MFEM finite element library (mfem.org). The scheme is fully implicit, solved with the Jacobian-free Newton-Krylov (JFNK) method with a physics-based preconditioning strategy. Our preconditioning strategy is a generalization of the physics-based preconditioning methods in Chacón et al. (2002) to adaptive, stabilized finite elements. Algebraic multigrid methods are used to invert sub-block operators to achieve scalability. A parallel adaptive mesh refinement scheme with dynamic load-balancing is implemented to efficiently resolve the multi-scale spatial features of the system. Our implementation uses the MFEM framework, which provides arbitrary-order polynomials and flexible adaptive conforming and non-conforming meshes capabilities. Results demonstrate the accuracy, efficiency, and scalability of the implicit scheme in the presence of large scale disparity. The potential of the AMR approach is demonstrated on an island coalescence problem in the high Lundquist-number regime (≥ 10 7 ) with the successful resolution of plasmoid instabilities and thin current sheets.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A new re-redistribution scheme for weighted state redistribution with adaptive mesh refinement

State redistribution (SRD) is a recently developed technique for stabilizing cut cells that result from finite-volume embedded boundary methods. SRD has been successfully applied to a variety of compressible and incompressible flow problems. When used in conjunction with adaptive mesh refinement (AMR), additional steps are needed to preserve the accuracy and conservation properties of the solution if the embedded boundary is not restricted to a single level of the mesh hierarchy. In this work, we extend the weighted state redistribution algorithm to cases where cut cells live at or near a coarse-fine interface within the domain. Here, we present numerical results that demonstrate that the algorithm is conservative when the coarse-fine interface intersects the embedded boundary. Additionally we compare the numerical solution of the Sod shock tube problem in an inclined cylinder with the analytic solution, and we compare the simulation of a shock hitting a cylindrical obstacle with experimental data. Finally we demonstrate the methodology for simulation of the multicomponent compressible Navier-Stokes equations in a piston-bowl geometry, and discuss the computational efficiency gained by not requiring the entire embedded boundary to be defined at the finest level.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Asymptotic-preserving semi-implicit finite volume scheme for extended magnetohydrodynamics

A Finite Volume (FV) scheme is developed for solving the extended magnetohydrodynamic (XMHD) equations, yielding accurate results in the ideal, resistive, and Hall MHD limits. This is accomplished by first re-writing the XMHD equations such that it allows the algorithm to retain the use of ideal MHD Riemann solvers and the constrained transport method to preserve divergence-free magnetic fields. Incorporation of electron inertia and displacement current introduces additional numerical stiffness which motivates a semi-implicit FV scheme that re-formulates the XMHD model as a relaxation system. The equations are then advanced in time using an explicit 2nd-order Runge–Kutta scheme with operator splitting applied to the implicit source term updates at each sub-stage. For additional numerical stability, a density-dependent slope limiter is implemented to increase flux diffusivity at low density regions where non-ideal effects become significant. The algorithm is subsequently implemented in a scalable adaptive mesh refinement (AMR) framework. As the new algorithm retains many aspects of the ideal MHD formulations, it asymptotes naturally to the ideal MHD limit. Moreover, it shows promising results at the resistive and Hall MHD limits. This is verified against reference test problems for ideal, resistive and Hall MHD.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Magnetism and spin-dependent transport phenomena across Verwey and Morin transitions in iron oxide/Pt bilayers

Understanding the influence of phase coexistence and phase transitions on spin transport properties in a ferromagnet/heavy metal (FM/HM) system is of utmost importance for spintronics. Here, we report a comprehensive investigation of the magnetic and spin transport properties of biphase iron oxide (BPIO = α-Fe 2 O 3 +Fe 3 O 4 )/Pt films over a wide temperature range, 10K ≤ T ≤ 300K. In-plane (IP) and out-of-plane (OOP) magnetometry and radio frequency transverse susceptibility measurements confirm the characteristic features of the Verwey and Morin transitions at T V ~ 120K and TM ~ 200 K, respectively. Further, anisotropic magnetoresistance (AMR) is observed in the BPIO film, which arises mainly from the spin polarized tunneling of conduction electrons between neighboring uniformly magnetized grains through the resistive grain boundary. Spin Hall magnetoresistance (SMR) and spin Hall anomalous Hall effect (SH-AHE) are detected in the BPIO/Pt films. Around the T V , the temperature evolution of SMR shows a sharp maximum, while SH-AHE exhibits a steep decrease. Both SMR and SH-AHE are strongly susceptible to the Verwey transition but the Morin transition, indicating that the interfacial magnetism of our BPIO/Pt film is dominated by the Fe 3 O 4 phase rather than the α-Fe 2 O 3 phase.

36 MATERIALS SCIENCE↗

Towards elastic in situ analysis for high-performance computing simulations

In situ analysis and visualization have grown increasingly popular for enabling direct access to data from high-performance computing (HPC) simulations. As a simulation progresses and interesting physical phenomena emerge, however, the data produced may become increasingly complex, and users may need to dynamically change the type and scale of in situ analysis tasks being carried out and consequently adapt the amount of resources allocated to such tasks. To date, none of the production in situ analysis frameworks offer such an elasticity feature, and for good reason: the assumption that the number of processes could vary during run time would force developers to rethink software and algorithms at every level of the in situ analysis stack. In this paper we present Colza, a data staging service with elastic in situ visualization capabilities. We demonstrate the use of Colza with the Deep Water Impact and the AMR-Wind simulations, coupling them with the ParaView Catalyst and Ascent in situ libraries, and show that Colza enables dynamic rescaling of these widely-used frameworks with no interruption to the simulation or staging service. Here, we highlight the challenges of enabling such elasticity, which requires overcoming these frameworks' reliance on MPI, using distinct engineering approaches, namely dependency injection and dependency overload. To the best of our knowledge, this work is the first to enable elastic in situ visualization capabilities for HPC applications on top of existing production analysis tools.

97 MATHEMATICS AND COMPUTING↗

Heat release surrogates for NH 3 /H 2 /N 2 –air premixed flames

The present study investigates the performance of NH, NH 2 , O-atom, and H-atom as heat release rate (HRR) surrogates for NH 3 /H 2 /N 2 –air premixed flame through simulations. The simulations are conducted across different pressures, reactant inlet temperatures, fuel blend compositions, and equivalence ratios. Cantera is used to simulate one-dimensional (1D) freely propagating flames to investigate the spatial correlations of the species with the HRR. PeleLMeX, a low-Mach direct numerical simulation (DNS) code with Adaptive Mesh Refinement (AMR), is used to simulate two-dimensional (2D) flame-vortex interactions to investigate the temporal correlations including stretch effects. Three different mechanisms (Jiang et al. 2020; Glarborg et al. 2018; Okafor et al. 2018) were considered in the 1D flame simulations, whereas only the Jiang mechanism was considered in the flame-vortex simulations. The HRR surrogate performance for the 2D flames is evaluated at two different locations: (1) the centerline and (2) the flame cusp. The cusp is defined as the region in the flame front with the greatest curvature and the centerline encounters the highest tangential strain rate. The 1D flame results suggest that, although there is not uniformly good spatial correlation for HRR across all flame conditions, NH is the best overall as a HRR surrogate for laminar flames. The 2D flame results, however, suggest that O-atom and H-atom have satisfactory temporal correlations at different conditions—the former for rich flames, the latter for high-pressure flames. Furthermore, these simulations provide guidance to experimental measurements of surrogate HRR markers in unsteady multi-dimensional flames using laser diagnostics to detect species such as NH, O-atom, and H-atom.

Ammonia↗

High resolution numerical simulations of methane pool fires using adaptive mesh refinement

The ability to accurately predict the structure and dynamics of pool fires using computational simulations is of great interest in a wide variety of applications, including accidental and wildland fires. However, the presence of physical processes spanning a broad range of spatial and temporal scales poses a significant challenge for simulations of such fires, particularly at conditions near the transition between laminar and turbulent flow. Here, in this study, we examine the transition to turbulence in methane pool fires using high-resolution simulations with multi-step finite rate chemistry, where adaptive mesh refinement (AMR) is used to directly resolve small-scale flow phenomena. We perform three simulations of methane pool fires, each with increasing diameter, corresponding to increasing inlet Reynolds and Richardson numbers. As the diameter increases, the flow transitions from organized vortex roll-up via the puffing instability to much more chaotic mixing associated with finger formation along the shear layer and core collapse near the inlet. These effects combine to create additional mixing close to the inlet, thereby enhancing fuel consumption and causing more rapid acceleration of the fluid above the pool. We also make comparisons between the transition to turbulence and core collapse in the present pool fires and in inert helium plumes, which are often used as surrogates for the study of buoyant reacting flows.

42 ENGINEERING↗

Genotypic analyses of IncHI2 plasmids from enteric bacteria

Incompatibility (Inc) HI2 plasmids are large (typically > 200 kb), transmissible plasmids that encode antimicrobial resistance (AMR), heavy metal resistance (HMR) and disinfectants/biocide resistance (DBR). To better understand the distribution and diversity of resistance-encoding genes among IncHI2 plasmids, computational approaches were used to evaluate resistance and transfer-associated genes among the plasmids. Complete IncHI2 plasmid (N - 667) sequences were extracted from GenBank and analyzed using AMRFinderPlus, IntegronFinder and Plasmid Transfer Factor database. The most common IncHI2-carrying genera included Enterobacter (N = 209), Escherichia (N = 208), and Salmonella (N = 204). Resistance genes distribution was diverse, with plasmids from Escherichia and Salmonella showing general similarity in comparison to Enterobacter and other taxa, which grouped together. Plasmids from Enterobacter and other taxa had a higher prevalence of multiple mercury resistance genes and arsenic resistance gene, arsC, compared to Escherichia and Salmonella. For sulfonamide resistance, sul1 was more common among Enterobacter and other taxa, compared to sul2 and sul3 for Escherichia and Salmonella. Similar gene diversity trends were also observed for tetracyclines, quinolones, β-lactams, and colistin. Over 99% of plasmids carried at least 25 IncHI2-associated conjugal transfer genes. These findings highlight the diversity and dissemination potential for resistance across different enteric bacteria and value of computational-based approaches for the resistance-gene assessment.

59 BASIC BIOLOGICAL SCIENCES↗

Anisotropic MagnetoMemristance

Abstract In the last decade, nanoscale resistive devices with memory have been the subject of intense study because of their possible use in brain-inspired computing. However, operational endurance is one of the limiting factors in the adoption of such technology. For this reason, we discuss the emergence of current-induced memristance in magnetic materials, known for their durability. We show analytically and numerically that a single ferromagnetic layer can possess GHz memristance, due to a combination of two factors: a current-induced transfer of angular momentum (Zhang-Li torque) and the anisotropic magnetoresistance (AMR). We term the resulting effect the anisotropic magneto-memristance (AMM). We connect the AMM to the topology of the magnetization state, within a simple model of a one-dimensional annulus-shaped magnetic layer, confirming the analytical results with micromagnetic simulations for permalloy. Our results open a new path towards the realization of single-layer magnetic memristive devices operating at GHz frequencies.

97 MATHEMATICS AND COMPUTING↗

Morphology of shocked lateral outflows in colliding hydrodynamic flows

Supersonic interacting flows occurring in phenomena, such as protostellar jets, give rise to strong shocks and have been demonstrated in several laboratory experiments. To study such colliding flows, we use the AstroBEAR AMR code to conduct hydrodynamic simulations in three dimensions. Here, we introduce variations in the flow parameters of density, velocity, and cross-sectional radius of the colliding flows in order to study the propagation and conical shape of the bow shock formed by collisions between two, not necessarily symmetric, hypersonic flows. We find that the motion of the interaction region is driven by imbalances in ram pressure between the two flows, while the conical structure of the bow shock is a result of shocked lateral outflows being deflected from the horizontal when the flows are of differing cross sections.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Wind farm response to mesoscale-driven coastal low level jets: a multiscale large eddy simulation study

Realistic atmospheric turbulence–wind farm interactions during coastal low-level jet (LLJ) events are captured using high-fidelity, mesoscale-driven large eddy simulations (LES) to understand wind turbine loads, wakes and overall performance. The simulation has been carried out using the ExaWind aeroelastic solver, AMR-Wind. The simulations have been compared against a baseline unstable case matching the wind speed, wind direction and TI at hub-height location. Results indicate that the LLJ has negative impacts on the turbine hub and tower loads, and opens up potential avenues for design load mitigation strategies.

17 WIND ENERGY↗

Structure of Offshore Low-Level Jet Turbulence and Implications to Mesoscale-to-Microscale Coupling

This paper explores realistic nonstationary atmospheric boundary layer (ABL) turbulence arising from nonstationarity at the mesoscale, particularly within offshore low-level jets with implications to offshore wind farms, using high-fidelity multiscale large-eddy simulations (LES). To this end, we analyzed the single-point turbulence statistical structure of a North-Atlantic offshore LLJ event simulated using high-resolution LES (AMR-Wind). The nonstationary LLJ is simulated using a mesoscale-to-microscale coupled (MMC) simulation procedure involving data assimilation of mesoscale velocity and temperature data from the Weather Research and Forecasting (WRF) model. Unlike the assimilation of mesoscale velocity data into the LES, the direct assimilation of temperature profiles had a strong impact on turbulence stratification, thereby causing erroneous predictions of turbulence both above and within the jet layer. Various approaches to mitigate this effect have resulted in multiple (four) variants of this MMC strategy. Outcomes from this work clearly show that the turbulence within the low-level jet is a strong function of the MMC approach as the turbulence structure within the low-level jet is dependent on the flux of residual turbulence from outside the jet, which in turn depends on the temperature forcing history. Additionally, the turbulence predicted by all these different methods (as well as the observation data) show similar deviations from equilibrium as evidenced by comparisons with idealized atmospheric turbulence structure obtained using the same numerical method. In general, we observe that the predicted LLJ turbulence tends to differ from canonical ABL turbulence with comparable shear. Particularly, the combination of shear and turbulence observed in such nonstationary low-level turbulence cannot be matched using equilibrium settings and therefore, represents a critical use-case for both testing and leveraging meso–micro coupling strategies.

17 WIND ENERGY↗

Bipolar planetary nebulae from outflow collimation by common envelope evolution

ABSTRACT The morphology of bipolar planetary nebulae (PNe) can be attributed to interactions between a fast wind from the central engine and the dense toroidal-shaped ejecta left over from common envelope (CE) evolution. Here we use the 3D hydrodynamic adaptive mesh refinement (AMR) code AstroBEAR to study the possibility that bipolar PN outflows can emerge collimated even from an uncollimated spherical wind in the aftermath of a CE event. The output of a single CE simulation via the smoothed particle hydrodynamics (SPH) code phantom serves as the initial conditions. Four cases of winds, all with high enough momenta to account for observed high momenta pre-PN outflows, are injected spherically from the region of the CE binary remnant into the ejecta. We compare cases with two different momenta and cases with no radiative cooling versus application of optically thin emission via a cooling curve to the outflow. Our simulations show that in all cases highly collimated bipolar outflows result from deflection of the spherical wind via the interaction with the CE ejecta. Significant asymmetries between the top and bottom lobes are seen in all cases. The asymmetry is strongest for the lower momentum case with radiative cooling. While real post-CE winds may be aspherical, our models show that collimation via ‘inertial confinement’ will be strong enough to create jet-like outflows even beginning with maximally uncollimated drivers. Our simulations reveal detailed shock structures in the shock-focused inertial confinement (SFIC) model and develop a lens-shaped inner shock that is a new feature of SFIC-driven bipolar lobes.

79 ASTRONOMY AND ASTROPHYSICS↗

General relativistic MHD simulations of non-thermal flaring in Sagittarius A*

Sgr A* exhibits regular variability in its multiwavelength emission, including daily X-ray flares and roughly continuous near-infrared (NIR) flickering. The origin of this variability is still ambiguous since both inverse Compton and synchrotron emission are possible radiative mechanisms. The underlying particle distributions are also not well constrained, particularly the non-thermal contribution. In this work, we employ the GPU-accelerated general relativistic magnetohydrodynamics code H-AMR to perform a study of flare flux distributions, including the effect of particle acceleration for the first time in high-resolution 3D simulations of Sgr A*. For the particle acceleration, we use the general relativistic ray-tracing code bhoss to perform the radiative transfer, assuming a hybrid thermal+non-thermal electron energy distribution. We extract ~60 h light curves in the sub-millimetre, NIR and X-ray wavebands, and compare the power spectra and the cumulative flux distributions of the light curves to statistical descriptions for Sgr A* flares. Our results indicate that non-thermal populations of electrons arising from turbulence-driven reconnection in weakly magnetized accretion flows lead to moderate NIR and X-ray flares and reasonably describe the X-ray flux distribution while fulfilling multiwavelength flux constraints. These models exhibit high rms per cent amplitudes, $\gtrsim 150{{\ \rm per\ cent}}$ both in the NIR and the X-rays, with changes in the accretion rate driving the 230 GHz flux variability, in agreement with Sgr A* observations.

79 ASTRONOMY AND ASTROPHYSICS↗

Cooling and instabilities in colliding flows

ABSTRACT Collisional self-interactions occurring in protostellar jets give rise to strong shocks, the structure of which can be affected by radiative cooling within the flow. To study such colliding flows, we use the AstroBEAR AMR code to conduct hydrodynamic simulations in both one and three dimensions with a power-law cooling function. The characteristic length and time-scales for cooling are temperature dependent and thus may vary as shocked gas cools. When the cooling length decreases sufficiently and rapidly, the system becomes unstable to the radiative shock instability, which produces oscillations in the position of the shock front; these oscillations can be seen in both the one- and three-dimensional cases. Our simulations show no evidence of the density clumping characteristic of a thermal instability, even when the cooling function meets the expected criteria. In the three-dimensional case, the nonlinear thin shell instability (NTSI) is found to dominate when the cooling length is sufficiently small. When the flows are subjected to the radiative shock instability, oscillations in the size of the cooling region allow NTSI to occur at larger cooling lengths, though larger cooling lengths delay the onset of NTSI by increasing the oscillation period.

79 ASTRONOMY AND ASTROPHYSICS↗

Tidal disruption discs formed and fed by stream–stream and stream–disc interactions in global GRHD simulations

When a star passes close to a supermassive black hole (BH), the BH’s tidal forces rip it apart into a thin stream, leading to a tidal disruption event (TDE). In this work, we study the post-disruption phase of TDEs in general relativistic hydrodynamics (GRHD) using our GPU-accelerated code h-amr. We carry out the first grid-based simulation of a deep-penetration TDE (β = 7) with realistic system parameters: a black hole-to-star mass ratio of 10 6 , a parabolic stellar trajectory, and a non-zero BH spin. We also carry out a simulation of a tilted TDE whose stellar orbit is inclined relative to the BH midplane. We show that for our aligned TDE, an accretion disc forms due to the dissipation of orbital energy with ~20 percent of the infalling material reaching the BH. The dissipation is initially dominated by violent self-intersections and later by stream–disc interactions near the pericentre. The self-intersections completely disrupt the incoming stream, resulting in five distinct self-intersection events separated by approximately 12 h and a flaring in the accretion rate. We also find that the disc is eccentric with mean eccentricity e ≈ 0.88. For our tilted TDE, we find only partial self-intersections due to nodal precession near pericentre. Although these partial intersections eject gas out of the orbital plane, an accretion disc still forms with a similar accreted fraction of the material to the aligned case. These results have important implications for disc formation in realistic tidal disruptions. For instance, the periodicity in accretion rate induced by the complete stream disruption may explain the flaring events from Swift J1644+57.

79 ASTRONOMY AND ASTROPHYSICS↗

Predicting antimicrobial susceptibility from the bacterial genome: A new paradigm for one health resistance monitoring

The laboratory identification of antibacterial resistance is a cornerstone of infectious disease medicine. In vitro antimicrobial susceptibility testing has long been based on the growth response of organisms in pure culture to a defined concentration of antimicrobial agents. By comparing individual isolates to wild type susceptibility patterns, strains with acquired resistance can be identified. Acquired resistance can also be detected genetically. After many decades of research, the inventory of genes underlying antimicrobial resistance (AMR) is well known for several pathogenic genera including zoonotic enteric organisms such as Salmonella and Campylobacter and continues to grow substantially for others. With the decline in costs for large scale DNA sequencing, it is now practicable to characterize bacteria using whole genome sequencing (WGS), including the carriage of resistance genes in individual microorganisms and those present in complex biological samples. With genomics we can generate comprehensive, detailed information on the bacterium, the mechanisms of antibiotic resistance, clues to its source, and the nature of mobile DNA elements by which resistance spreads. These developments point to a new paradigm for antimicrobial resistance detection and tracking for both clinical and public health purposes.

59 BASIC BIOLOGICAL SCIENCES↗

Multidimensional Numerical Modeling of Combustion Dynamics in a Non-Premixed Rotating Detonation Engine With Adaptive Mesh Refinement

In the present work, a novel computational fluid dynamics (CFD) methodology was developed to simulate full-scale non-premixed rotating detonation engines (RDEs). A unique feature of the modeling approach was the incorporation of adaptive mesh refinement (AMR) to achieve a good trade-off between model accuracy and computational expense. Here, unsteady Reynolds-averaged Navier–Stokes (RANS) simulations were performed for an Air Force Research Laboratory (AFRL) non-premixed RDE configuration with hydrogen as fuel and air as the oxidizer. The finite-rate chemistry model, along with a ten-species detailed kinetic mechanism, was employed to describe the H 2 -Air combustion chemistry. Three distinct operating conditions were simulated, corresponding to the same global equivalence ratio of unity but different fuel/air mass flowrates. For all conditions, the capability of the model to capture essential detonation wave dynamics was assessed. An exhaustive verification and validation study was performed against experimental data in terms of a number of waves, wave frequency, wave height, reactant fill height, oblique shock angle, axial pressure distribution in the channel, and fuel/air plenum pressure. The CFD model was demonstrated to accurately predict the sensitivity of these wave characteristics to the operating conditions, both qualitatively and quantitatively. A comprehensive heat release analysis was also conducted to quantify detonative versus deflagrative burning for the three simulated cases. The present CFD model offers a potential capability to perform rapid design space exploration and/or performance optimization studies for realistic full-scale RDE configurations.

42 ENGINEERING↗