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NASA NTRS2010

Multiscale Simulations of Magnetic Island Coalescence

We describe a new interactive parallel Adaptive Mesh Refinement (AMR) framework written in the Python programming language. This new framework, PyAMR, hides the details of parallel AMR data structures and algorithms (e.g., domain decomposition, grid partition, and inter-process communication), allowing the user to focus on the development of algorithms for advancing the solution of a systems of partial differential equations on a single uniform mesh. We demonstrate the use of PyAMR by simulating the pairwise coalescence of magnetic islands using the resistive Hall MHD equations. Techniques for coupling different physics models on different levels of the AMR grid hierarchy are discussed.

Dorelli, John C.↗

NASA NTRS2012

Detached Eddy Simulation of the UH-60 Rotor Wake Using Adaptive Mesh Refinement

Time-dependent Navier-Stokes flow simulations have been carried out for a UH-60 rotor with simplified hub in forward flight and hover flight conditions. Flexible rotor blades and flight trim conditions are modeled and established by loosely coupling the OVERFLOW Computational Fluid Dynamics (CFD) code with the CAMRAD II helicopter comprehensive code. High order spatial differences, Adaptive Mesh Refinement (AMR), and Detached Eddy Simulation (DES) are used to obtain highly resolved vortex wakes, where the largest turbulent structures are captured. Special attention is directed towards ensuring the dual time accuracy is within the asymptotic range, and verifying the loose coupling convergence process using AMR. The AMR/DES simulation produced vortical worms for forward flight and hover conditions, similar to previous results obtained for the TRAM rotor in hover. AMR proved to be an efficient means to capture a rotor wake without a priori knowledge of the wake shape.

Chaderjian, Neal M.↗

NASA NTRS2018

Using Adaptive Mesh Refinement to Study Grid Resolution Effects for Shock-Boundary Layer Interactions

Adaptive Mesh Refinement (AMR) promises a much more computationally efficient means to obtain a discrete approximation to a continuous boundary value problem of a specified accuracy than classic isotropic grid refinement. The AMR capability of OVERFLOW (a computational fluid dynamics (CFD) code) is utilized to provide estimates of the exact analytical solutions to problems of interest to turbulence modeling. Predictions of surface pressure and skin friction, essentially the state of stress at the surface, shows little difference with grids believed to be "grid resolved." Velocity profiles, on the other hand, show marked differences in flows with shocks. The AMR method, as implemented in OVERFLOW 2.2k, appears to provide the ability to produce arbitrarily accurate solutions at a predictable cost much smaller than classic uniform mesh refinement.

Turbulence Modeling↗

NASA NTRS2018

Using Adaptive Mesh Refinement to Study Grid Resolution Effects for Shock/Boundary-Layer Interactions

Adaptive Mesh Refinement (AMR) promises a much more computationally efficient meansto obtain a discrete approximation to a continuous boundary value problem of a specifiedaccuracy than classic isotropic grid refinement. The AMR capability of OVERFLOW is utilizedto provide estimates of the exact analytical solutions to problems of interest to turbulencemodeling. Predictions of surface pressure and skin friction, essentially the state of stress at thesurface, shows little difference with grids believed to be "grid resolved." Velocity profiles, on theother hand, show marked differences in flows with shocks. The AMR method, as implementedin OVERFLOW2.2k, appears to provide the ability to produce arbitrarily accurate solutionsat a predictable cost much smaller than classic uniform mesh refinement.

Adaptive Mesh Refinement↗

NASA NTRS2018

Detection of Antimicrobial Resistance Genes Associated With the International Space Station Environmental Surfaces

Antimicrobial resistance (AMR) is a global health issue. In an effort to minimize this threat to astronauts, who may be immunocompromised and thus at a greater risk of infection from antimicrobial resistant pathogens, a comprehensive study of the ISS “resistome’ was conducted. Using whole genome sequencing (WGS) and disc diffusion antibiotic resistance assays, 9 biosafety level 2 organisms isolated from the ISS were assessed for their antibiotic resistance. Molecular analysis of AMR genes from 24 surface samples collected from the ISS during 3 different sampling events over a span of a year were analyzed with Ion AmpliSeq™ and metagenomics. Disc diffusion assays showed that Enterobacter bugandensis strains were resistant to all 9 antibiotics tested and Staphylococcus haemolyticus being resistant to none. Ion AmpliSeq™ revealed that 123 AMR genes were found, with those responsible for beta-lactam and trimethoprim resistance being the most abundant and widespread. Using a variety of methods, the genes involved in antimicrobial resistance have been examined for the first time from the ISS. This information could lead to mitigation strategies to maintain astronaut health during long duration space missions when return to Earth for treatment is not possible.

Antimicrobial resistance↗

DOE OSTI2025

Inching toward the QCD axions with axion magnetic resonance in helioscopes

Utilizing a helical magnet profile to enhance axion-photon conversion showed great promise in laboratory searches for high axion masses. We extend the mechanism, known as the axion-magnetic resonance (AMR), from laser experiments to axion helioscopes and demonstrate its potential in covering QCD axion parameter space. Specifically, we apply AMR to the CAST experiment legacy, make projections for the upcoming IAXO experiment, and assess its implications for both axion-like particles and QCD axions. We observe considerable improvement in the experiment’s sensitivity reach in all cases.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Aeromonas in South Asia: genomic insights into an environmental pathogen and reservoir of antimicrobial resistance

Aeromonads are an ecologically versatile group of bacteria that cause infections in aquatic animals and are recognised as emerging human pathogens. Despite this, our understanding of Aeromonas diversity, especially the relationship between clinical and environmental strains, remains limited. Here, we present a genomic analysis of the Aeromonas genus, comprising 1853 genomes, and a detailed comparison of clinical and environmental strains from South Asia, including 996 newly sequenced genomes from Bangladesh and India. Phylogenetic analyses revealed that Aeromonas is a highly diverse genus, with no distinct clade separating clinical and environmental isolates. We identified 28 Aeromonas species and 905 novel sequence types, comprising 72.5% of the genomes. Notably, we show a high incidence of antimicrobial resistance (AMR) genes across all isolates, including against front and last-line antibiotics. Finally, we highlight frequent misidentification of Aeromonas as Vibrio cholerae, which is relevant to cholera-endemic regions where both genera co-exist and are associated with diarrhoeal disease. Our study underscores Aeromonas as an important environmental AMR reservoir and emerging multi-species pathogen capable of spilling over into human populations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

A High-Quality Workflow for Multi-Resolution Scientific Data Reduction and Visualization

Multi-resolution methods such as Adaptive Mesh Refinement (AMR) can enhance storage efficiency for HPC applications generating vast volumes of data. However, their applicability is limited and cannot be universally deployed across all applications. Furthermore, integrating lossy compression with multi-resolution techniques to further boost storage efficiency encounters significant barriers. To this end, we introduce an innovative workflow that facilitates high-quality multi-resolution data compression for both uniform and AMR simulations. Initially, to extend the usability of multi-resolution techniques, our workflow employs a compression-oriented Region of Interest (ROI) extraction method, transforming uniform data into a multi-resolution format. Subsequently, to bridge the gap between multi-resolution techniques and lossy compressors, we optimize three distinct compressors, ensuring their optimal performance on multi-resolution data. These optimizations can improve the compression ratio of SOTA approaches by up to 3.3× under the same data quality loss. Lastly, we incorporate an advanced uncertainty visualization method into our workflow to understand the potential impacts of lossy compression. Experimental evaluation demonstrates that our workflow achieves significant compression quality improvements.

Wang, Daoce↗

DOE OSTI2024

Towards exascale for wind energy simulations

We examine large-eddy-simulation modeling approaches and computational performance of two open-source computational fluid dynamics codes for the simulation of atmospheric boundary layer flows that are of direct relevance to wind energy production. The first code, NekRS, is a high-order, unstructured-grid, spectral element code. The second code, AMR-Wind, is a second-order, block-structured, finite-volume code with adaptive mesh refinement capabilities. The objective of this study is to co-develop these codes in order to improve model fidelity and performance for each. These features will be critical for running ABL-based applications such as wind farm analysis on advanced computing architectures. To this end, we investigate the performance of NekRS and AMR-Wind on the Oak Ridge Leadership Facility supercomputers Summit, using 4 to 800 nodes (24 to 4,800 NVIDIA V100 GPUs), and Crusher, the testbed for the Frontier exascale system, using 18 to 384 Graphics Compute Dies on AMD MI250X GPUs. We compare strong- and weak-scaling capabilities, linear solver performance, and time to solution. We also identify leading inhibitors to parallel scaling.

17 WIND ENERGY↗

DOE OSTI2025

Modeling the Interaction of Laser-Produced Proton Beams with Matter

A major goal of this project is to significantly increase our understanding of isochoric heating of matter using laser produced proton beams, and the associated high energy density (HED) and warm dense matter (WDM) regimes generated. This will benefit research fields such as planetary science, fusion energy, plasma physics, and material science. For example, it will enhance our understanding of WDM properties of iron and silica under conditions encountered in planetary interiors and diagnostic components in fusion devices exposed to high fluxes of energetic plasma ions. The project is motivated by recent experiments that irradiated Si targets with proton beams generated by the 20 TW-laser at the SLAC MEC end-station. The HED/WDM states are probed using the 50 fs hard X-rays available in the 3rd harmonic of the LCLS. As part of this project, results from the phase contrast X-ray imaging, which shows the generation of compression waves that produces rear surface spallation, are compared with results from the 3D multi-physics multi- material code, PISALE, that combines Arbitrary Lagrangian-Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR). This comparison required modifications to several physics models in the PISALE (Pacific Island Structured-AMR with ALE) code. An important aspect of this project is the continued training of graduate students in HED physics and in conducting complex multiphysics simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1976

Applications Study of Aero-Maneuvering Orbit-to-Orbit Shuttle (AMOOS), Executive Summary

Preliminary designs and the supporting analysis for both the Aeromaneuvering Orbit-to-Orbit Shuttle (AMOOS) and the Aeromaneuvering Recovery System (AMRS) are presented. The AMOOS design is shown to yield from twice to almost three times the high energy, round-trip payloads as a purely propulsive vehicle of the same weight. Typically AMOOS can perform a crew rotation mission to equatorial geosynchronous orbit in one space shuttle launch. The flight test program analysis modeled parameters such as maximum dynamic pressure, heating rates, guidance, stability and recovery. Two model flight schedules were developed, one consisting of four flights and the other of two flights. The former is considered a very low risk, high information return program whereas the latter is a minimal cost program consistent with reasonable data returns and chance of success. The AMOOS and AMRS guidance scheme developed using linear regulator theory proved a precise and accurate guidance scheme. Both it and a classical linear system's based scheme were evaluated using 65 simulated trajectories in which the position in the entry corridor and the atmospheric density were varied randomly.

White, J.↗

NASA NTRS1984

Clear air turbulence avoidance using an airborne microwave radiometer

The avoidance of Clear Air Turbulence (CAT) is theoretically possible by selecting flight levels that are a safe distance from the tropopause and inversion layers. These favored sites for CAT generation can be located by an 'airborne microwave radiometer' (AMR) passive sensor system that measures altitude temperature profiles. A flight evaluation of the AMR sensor shows that most CAT could be avoided by following sensor-based advisories. Some limitations still exist for any hypothetical use of the sensor. The principal need is to augment the sensor's 'where' advisories to include useful 'when' forecasts.

Gary, B. L.↗

NASA NTRS1993

A parallel adaptive mesh refinement algorithm

Over recent years, Adaptive Mesh Refinement (AMR) algorithms which dynamically match the local resolution of the computational grid to the numerical solution being sought have emerged as powerful tools for solving problems that contain disparate length and time scales. In particular, several workers have demonstrated the effectiveness of employing an adaptive, block-structured hierarchical grid system for simulations of complex shock wave phenomena. Unfortunately, from the parallel algorithm developer's viewpoint, this class of scheme is quite involved; these schemes cannot be distilled down to a small kernel upon which various parallelizing strategies may be tested. However, because of their block-structured nature such schemes are inherently parallel, so all is not lost. In this paper we describe the method by which Quirk's AMR algorithm has been parallelized. This method is built upon just a few simple message passing routines and so it may be implemented across a broad class of MIMD machines. Moreover, the method of parallelization is such that the original serial code is left virtually intact, and so we are left with just a single product to support. The importance of this fact should not be underestimated given the size and complexity of the original algorithm.

Quirk, James J.↗

NASA NTRS1995

Adaptively-refined overlapping grids for the numerical solution of systems of hyperbolic conservation laws

Adaptive mesh refinement (AMR) in conjunction with higher-order upwind finite-difference methods have been used effectively on a variety of problems in two and three dimensions. In this paper we introduce an approach for resolving problems that involve complex geometries in which resolution of boundary geometry is important. The complex geometry is represented by using the method of overlapping grids, while local resolution is obtained by refining each component grid with the AMR algorithm, appropriately generalized for this situation. The CMPGRD algorithm introduced by Chesshire and Henshaw is used to automatically generate the overlapping grid structure for the underlying mesh.

Brislawn, Kristi D.↗

NASA NTRS1995

Adaptive Mesh Refinement in Curvilinear Body-Fitted Grid Systems

To be truly compatible with structured grids, an AMR algorithm should employ a block structure for the refined grids to allow flow solvers to take advantage of the strengths of unstructured grid systems, such as efficient solution algorithms for implicit discretizations and multigrid schemes. One such algorithm, the AMR algorithm of Berger and Colella, has been applied to and adapted for use with body-fitted structured grid systems. Results are presented for a transonic flow over a NACA0012 airfoil (AGARD-03 test case) and a reflection of a shock over a double wedge.

Steinthorsson, Erlendur↗

NASA NTRS1998

LOOPREF: A Fluid Code for the Simulation of Coronal Loops

This report documents the code LOOPREF. LOOPREF is a semi-one dimensional finite element code that is especially well suited to simulate coronal-loop phenomena. It has a full implementation of adaptive mesh refinement (AMR), which is crucial for this type of simulation. The AMR routines are an improved version of AMR1D. LOOPREF's versatility makes is suitable to simulate a wide variety of problems. In addition to efficiently providing very high resolution in rapidly changing regions of the domain, it is equipped to treat loops of variable cross section, any non-linear form of heat conduction, shocks, gravitational effects, and radiative loss.

deFainchtein, Rosalinda↗

NASA NTRS1998

Polar Plasma Wave Observations in the Auroral Region and Polar Cap

Auroral kilometric radiation (AKR), sometimes associated with auroral myriametric radiation (AMR), has been observed by the plasma wave instrument on board Polar on almost every northern hemisphere pass. High spectral resolution plots of the AKR obtained by the wide-band receiver of the plasma wave instrument on board the spacecraft often show discrete, negative-slope striations each extending over a period of several seconds. A preliminary survey of over 4000 spectrograms (each for 48 seconds of data) indicates that the striations are seen in the northern hemisphere near apogee about 5% of the time. The frequency range is 40 kHz less than f less than 100 kHz, but a few observations of signatures have been made at higher frequency (f less than 225 khz. The frequency drift rates R, are similar ranging from -9.0 kHz/sec less than R less than -1.0 kHz/sec. No data is currently available for perigee (southern hemisphere) passes. The paucity of positive-slope features may be due to the location of the satellite at altitudes well above the AKR source region. Past studies have suggested these features are due to AKR wave growth stimulated by the propagation of electromagnetic ion cyclotron waves travelling up (-R) or down (+R) the field line, through the source region. High-resolution waveform data from both Polar and FAST show the presence of solitary waves in the auroral region which may also be a source of these striations. AMR is seen as diffuse emission associated with, but at lower frequency than the lower AKR. Direction finding of these emissions is not conclusive, but for one case, they have a source region distinct from the magnetic field line containing the AKR source, but possibly associated with the auroral cavity density gradient.

Menietti, J. D.↗

NASA NTRS2007

Orbit Processing and Analysis of a GEO Class of High Area-to-Mass Debris Objects

A population of recently discovered deep space objects is thought to be debris having origins from sources in the geosynchronous orbit (GEO) belt. Observations have been presented indicating that these objects have area-to-mass ratios (AMR's) of anywhere from 1's to 10's of m(exp 2)/kg, and thus would explain the observed migration of eccentricity (0.1-0.6) and inclination that distinguishes their orbital characteristics. The solar radiation perturbations on orbital period, inclination and eccentricity over a 20 year period for AMR's of 0.01, 1, 10 and 20 m(exp 2)/kg, are shown in the figures. There is a heightened interest in the international community due to the large number and small size of these objects, as they pose a hazard to active satellites operating in the vicinity of the GEO belt.

Kelecy, Tom↗