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Results for “Structured Adaptive Mesh Refinement”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Betelgeuse as a Merger of a Massive Star with a Companion

We investigate the merger between a 16M ⊙ star, on its way to becoming a red supergiant (RSG), and a 4M ⊙ main-sequence companion. Our study employs three-dimensional hydrodynamic simulations using the state-of-the-art adaptive mesh refinement code Octo-Tiger. The initially corotating binary undergoes interaction and mass transfer, resulting in the accumulation of mass around the companion and its subsequent loss through the second Lagrangian point (L2). The companion eventually plunges into the envelope of the primary, leading to its spin-up and subsequent merger with the helium core. We examine the internal structural properties of the post-merger star, as well as the merger environment and the outflow driven by the merger. Our findings reveal the ejection of approximately ∼0.6 M ⊙ of material in an asymmetric and somewhat bipolar outflow. We import the post-merger stellar structure into the MESA stellar evolution code to model its long-term nuclear evolution. In certain cases, the post-merger star exhibits persistent rapid equatorial surface rotation as it evolves in the H–R diagram toward the observed location of Betelgeuse. These cases demonstrate surface rotation velocities of a similar magnitude to those observed in Betelgeuse, along with a chemical composition resembling that of Betelgeuse. In other cases, efficient rotationally induced mixing leads to slower surface rotation. This pioneering study aims to model stellar mergers across critical timescales, encompassing dynamical, thermal, and nuclear evolutionary stages.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

A space-time parallel algorithm with adaptive mesh refinement for computational fluid dynamics

This work describes a space-time parallel algorithm with space-time adaptive mesh refinement (AMR). AMR with subcycling is added to multigrid reduction-in-time (MGRIT) in order to provide solution efficient adaptive grids with a reduction in work performed on coarser grids. This algorithm is achieved by integrating two software libraries: XBraid (Parallel time integration with multigrid. https://computation.llnl.gov/projects/parallel-timeintegration-multigrid) and Chombo (Chombo software package for AMR applications—design document, 2014). The former is a parallel time integration library using multigrid and the latter is a massively parallel structured AMR library. Employing this adaptive space-time parallel algorithm is Chord (Comput Fluids 123:202–217, 2015), a computational fluid dynamics (CFD) application code for solving compressible fluid dynamics problems. For the same solution accuracy, speedups are demonstrated from the use of space-time parallelization over the time-sequential integration on Couette flow and Stokes’ second problem. On a transient Couette flow case, at least a 1.5× speedup is achieved, and with a time periodic problem, a speedup of up to 13.7× over the time-sequential case is obtained. In both cases, the speedup is achieved by adding processors and exploring additional parallelization in time. The numerical experiments show the algorithm is promising for CFD applications that can take advantage of the time parallelism. Future work will focus on improving the parallel performance and providing more tests with complex fluid dynamics to demonstrate the full potential of the algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) [SWR-23-37]

MARBLES (Multi-scale Adaptively Refined Boltzmann LatticE Solver) is an open-source computational fluid dynamics package powered by the lattice Boltzmann equations and built on AMReX. In the lattice Boltzmann method, local collisions between meso-scale fictitious particles drive the governing equations which enables MARBLES to easily simulate flow around complex and/or moving geometry without the generation of a body-conforming mesh. Using AMReX data structures and operations ensures a high level of computational performance and parallel scaling on heterogenous architectures while also naturally supporting locally enhanced grid resolution and fidelity through automatic mesh refinement. New domains and problem definitions are easily specified through an input file with examples and guidance on all options and variables provided in the MARBLES documentation.

Henry de Frahan, Marc↗
DOE OSTI2024

Properties of molecular clumps and cores in colliding magnetized flows

ABSTRACT We simulate the formation of molecular clouds in colliding flows of warm neutral medium with the adaptive mesh refinement code flash in eight simulations with varying initial magnetic field strength, between 0.01–5 μG. We include a chemical network to treat heating and cooling and to follow the formation of molecular gas. The initial magnetic field strength influences the fragmentation of the forming cloud because it prohibits motions perpendicular to the field direction and hence impacts the formation of large-scale filamentary structures. Molecular clump and core formation occurs anyhow. We identify 3D clumps and 3D cores, which are defined as connected, CO-rich regions. Additionally, 3D cores are heavily shielded. While we do not claim those 3D objects to be directly comparable to observations, this enables us to analyse their full virial state. With increasing field strength, we find more fragments with a smaller average mass; yet the dynamics of the forming clumps and cores only weakly depends on the initial magnetic field strength. The molecular clumps are mostly unbound, probably transient objects, which are weakly confined by ram pressure or thermal pressure, indicating that they are swept up by the turbulent flow. They experience significant fluctuations in the mass flux through their surface, such that the Eulerian reference frame shows a dominant time-dependent term due to their indistinct nature. We define the cores to encompass highly shielded molecular gas. Most cores are in gravitational-kinetic equipartition and are well described by the common virial parameter $\alpha _\mathrm{vir}$, while some undergo minor dispersion by kinetic surface effects.

Weis, M. (ORCID:0000000256838860)↗
DOE OSTI2022

Hurricane‐Like Vortices in Conditionally Unstable Moist Convection

Abstract This study investigates the emergence of hurricane‐like vortices in idealized simulations of rotating moist convection. A Boussinesq atmosphere with simplified thermodynamics for phase transitions is forced by prescribing the temperature and humidity at the upper and lower boundaries. The governing equations are solved numerically using a variable‐density incompressible Navier‐Stokes solver with adaptive mesh refinement to explore the behavior of moist convection under a broad range of conditions. In the absence of rotation, convection aggregates into active patches separated by large unsaturated regions. Rotation modulates this statistical equilibrium state so that the self‐aggregated convection organizes hurricane‐like vortices. The warm and saturated air converges to the center of the vortices, and the latent heat released through the upwelling, forms the warm core structure. These hurricane‐like vortices share characteristics similar to tropical cyclones in the earth's atmosphere. The hurricane‐like vortices occur under conditionally unstable conditions where the potential energy given at the boundaries is large enough, corresponding to a moderate rate of rotation. This regime shares many similar characteristics to the tropical atmosphere indicating that the formation of intense meso‐scale vortices is a general characteristic of rotating moist convection. The model used here does not include any interactions with radiation, wind‐evaporation feedback, or cloud microphysics, indicating that, while these processes may be relevant for tropical cyclogenesis in the Earth atmosphere, they are not its primary cause. Instead, our results confirm that the formation and maintenance of hurricane‐like vortices involve a combination of atmospheric dynamics under the presence of rotation and of phase transitions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Clumpy structures within the turbulent primordial cloud

ABSTRACT The primordial clouds in the mini-haloes hatch the first generation stars of the Universe, which play a crucial role in cosmic evolution. In this paper, we investigate how turbulence impacts the structure of primordial star-forming clouds. Previous cosmological simulations of the first star formation predicted a typical mass of around $\mathrm{ 100 \, M_\odot }$. This conflicts with recent observations of extremely metal-poor stars, suggesting a lower mass scale of about $\mathrm{25 \, M_\odot }$. The discrepancy may arise from unresolved turbulence in the star-forming cloud, driven by primordial gas accretion during mini-halo formation in the previous simulations. To quantitatively examine the turbulence effect on the primordial cloud formation, we employ the adaptive mesh refinement code Enzo to model the gas cloud with primordial composition, including artificially driven turbulence on the cloud scale and relevant gas physics. This artificially driven turbulence utilizes a stochastic forcing model to mimic the unresolved turbulence inside mini-haloes. Our results show that the turbulence with high Mach number and compressional mode effectively fragments the cloud into several clumps, each with dense cores of $\mathrm{22.7 - 174.9 \, M_\odot }$ that undergo Jeans instability to form stars. Fragmentation caused by intense and compressive turbulence prevents a runaway collapse of the cloud. The self-bound clumps with smaller masses in the turbulent primordial clouds suggest a possible pathway to decrease the theoretical mass scale of the first stars, further reconciling the mass discrepancy between simulations and observations.

Astronomy & Astrophysics↗
DOE OSTI2020

Parallelization and Performance Portability in Hydrodynamics Codes

With the eve of Exascale computing, performance and portability are at the forefront of all scientific codes. Adding more cores and more energy to a system is no longer a sustainable way to achieve performance, and extra effort must now be made to improve performance in all areas of code and code development. Using hydrodynamic codes as a basis, this work explores numerous techniques to achieve performance in different ways. Adaptive mesh refinement (AMR) is a necessary technique to improve memory optimization in mesh-based simulations. However it is invasive and conventionally difficult to integrate into existing applications, so we present a new branch of AMR to create a smooth transition to these optimizations, which not only improves performance, but also greatly reduces developer effort. We introduce the concept of this improvement as Phantom-Cell AMR, and assess theoretically the improvements, as well as present an application of its use. Other work included involves and investigation into an efficient data structure that ensures optimal memory layout for cache performance, with a target of making codes performant and portable across all architectures. All of the work targets both performance and portability, not just on CPU hardware, but specifically across GPU architectures. Parallel performance is key to all of the methods presented, but the research makes a great effort to improve the portability of all applications to prepare for current high performance computing systems and those on the horizon.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Hydrodynamic simulations of white dwarf–white dwarf mergers and the origin of R Coronae Borealis stars

We study the properties of double white dwarf (DWD) mergers by performing hydrodynamic simulations using the new and improved adaptive mesh refinement code OCTO-TIGER. We follow the orbital evolution of DWD systems of mass ratio $q=0.7$ for tens of orbits until and after the merger to investigate them as a possible origin for R Coronae Borealis (RCB) type stars. We reproduce previous results, finding that during the merger, the helium WD donor star is tidally disrupted within 20–80 min since the beginning of the simulation onto the accretor carbon–oxygen WD, creating a high temperature shell around the accretor. We investigate the possible helium burning in this shell and the merged object’s general structure. Specifically, we are interested in the amount of oxygen-16 dredged-up from the accretor to the hot shell and the amount of oxygen-18 produced. This is critical as the discovery of very low oxygen-16 to oxygen-18 ratios in RCB stars pointed out the merger scenario as a favourable explanation for their origin. A small amount of hydrogen in the donor may help keep the oxygen-16 to oxygen-18 ratios within observational bounds, even if moderate dredge-up from the accretor occurs. In addition, we perform a resolution study to reconcile the difference found in the amount of oxygen-16 dredge-up between smoothed-particle hydrodynamics and grid-based simulations.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

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↗
DOE OSTI2026

Coupling Noah-Multiparameterization land-surface Model with Energy Research and Forecasting Model

The Energy Research and Forecasting (ERF) model is a high-performance atmospheric model built on the AMReX adaptive mesh refinement (AMR) framework, enabling efficient simulations on heterogeneous computing platforms that combine multicore processors with hardware accelerators. To support land–atmosphere interactions within ERF’s AMR-based environment, a land-surface model must be capable of operating directly on hierarchically refined meshes. In this work, we present a methodology for coupling the Fortran-based Noah-Multiparameterization (Noah-MP) land-surface model with ERF’s C++ codebase. Rather than rewriting Noah-MP, we construct a Fortran–C interoperability layer using CodeScribe, a tool that leverages large language models (LLMs) to automate the generation of interface code. CodeScribe applies structured prompting techniques to generate bindings that support efficient data exchange and function calls between ERF and Noah-MP. The coupling framework also incorporates AMR-aware data handling strategies, allowing NoahMP to operate seamlessly within ERF’s hierarchical mesh structure. This work provides a structured approach for integrating legacy Fortran models into modern C++-based modeling systems using LLM-assisted code generation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Computational Study of Variable Fuel-Air Ratio and Hydrogen Doping in a Rotating Detonation Engine

Rotating detonation engines (RDEs) hold great promise as a technology for powering aviation engines. The pressure gain that results from continuously traversing detonation waves enables high theoretical performance compared to deflagration-based combustion. However, the harsh operating conditions inside an RDE restrict the availability of suitable experimental diagnostics to study these systems in detail and the range of spatial and temporal scales render numerical simulations of these systems difficult. In this study, we have combined adaptive mesh refinement and a robust shock-capturing approach to study RDE systems computationally using the compressible, reactive solver PeleC. Multi-species transport along with compressible Navier-Stokes equations are solved in the model along with finite-rate chemistry. Complex geometries are represented using an embedded boundary method with second-order spatial accuracy and the system is evolved in time using a second-order Runge-Kutta method. We present studies of a methane-air RDE system that is doped with varying levels of hydrogen. Our analysis focusses on how fuel mixture and doping levels effect the detonation flame structure and the generation of multiple wave modes.

ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

Gravitation and Mesh Adaption

The Gravitation and Mesh Adaptation (GaMA) toolbox consists of a set of Matlab classes for modeling the environment around asteroids and comets. A variety of gravitational models and supporting algorithms from are consolidated alongside a custom meshing utility tailored for the application. This allows the user to work within a single streamlined environment to import and manipulate surface definitions, probe the dynamical environment, integrate trajectories, and post-process results. For other applications, modified surface meshes can be exported. Gravity Models: 1) Werner's analytic polyhedron model 2) Mascon model 3) Gottlieb's spherical harmonic model 4) Approximate polyhedron models 5) Curvilinear surface models 6) Custom composite models Meshing Features: 1) Array-based half-edge data structure 2) Supports curvilinear surface definitions up to degree 4 3) Ray-tracing 4) Coarsening 5) Feature-based refinement 6) Projection 7) Smoothing 8) Mesh quality validity tests 9) Mesh repair Additional Features: 1) Solar radiation pressure model 2) Distant 3rd body model 3) Collision detection 4) Trajectory integration and post-processing 5) Visualization of surface fields

Pearl, Jason↗
DOE OSTI2025

Robust Implicit Adaptive Low Rank Time-Stepping Methods for Matrix Differential Equations

In this work, we develop implicit rank-adaptive schemes for time-dependent matrix differential equations. The dynamic low rank approximation (DLRA) is a well-known technique to capture the dynamic low rank structure based on Dirac–Frenkel time-dependent variational principle. In recent years, it has attracted a lot of attention due to its wide applicability. Our schemes are inspired by the three-step procedure used in the rank adaptive version of the unconventional robust integrator (the so called BUG integrator) (Ceruti et al. in BIT Numer Math 62(4):1149–1174, 2022) for DLRA. First, a prediction (basis update) step is made computing the approximate column and row spaces at the next time level. Second, a Galerkin evolution step is invoked using an implicit solves for the small core matrix. Finally, a truncation is made according to a prescribed error threshold. Since the DLRA is evolving the differential equation projected on to the tangent space of the low rank manifold, the error estimate of the BUG integrator contains the tangent projection (modeling) error which cannot be easily controlled by mesh refinement. This can cause convergence issue for equations with cross terms. To address this issue, we propose a simple modification, consisting of merging the row and column spaces from the explicit step truncation method together with the BUG spaces in the prediction step. In addition, we propose an adaptive strategy where the BUG spaces are only computed if the residual for the solution obtained from the prediction space by explicit step truncation method, is too large. Here, we prove stability and estimate the local truncation error of the schemes under assumptions. We benchmark the schemes in several tests, such as anisotropic diffusion, solid body rotation and the combination of the two, to show robust convergence properties.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The effect of saturated thermal conduction on clouds in a hot plasma

We numerically investigate the internal evolution of multiphase clouds, which are at rest with respect to an ambient, highly ionized medium (HIM) representing the hot component of the circumgalactic medium. Time-dependent saturated thermal conduction and its implications like condensation rates and mixing efficiency are assessed in multiphase clouds. Our simulations are carried out by using the adaptive mesh refinement code FLASH. The model clouds are initially in both hydrostatic and thermal equilibrium and are in pressure balance with the HIM. Thus, they have steep gradients in both temperature and density at the interface to HIM leading to non-negligible thermal conduction. Several physical processes are considered numerically or semi-analytically: thermal conduction, radiative cooling and external heating of gas, self-gravity, mass diffusion, and dissociation of molecules and ionization of atoms. It turns out that saturated thermal conduction triggers a continuous condensation irrespective of cloud mass. Dynamical interactions with ambient HIM all relate to the radial density gradient in the clouds: (1) mass flux due to condensation is the higher the more homogeneous the clouds are; (2) mixing of condensed gas with cloud gas is easier in low-mass clouds, because of their shallower radial density gradient; and thus (3) accreted gas is distributed more efficiently. A distinct and sub-structured transition zone forms at the interface between cloud and HIM, which starts at smaller radii and is much narrower as deduced from analytical theory.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Numerical Study on the Effect of Methane Doping in Hydrogen-Air Rotating Detonation Engines for Various Temperatures and Pressures

Rotating detonation engines (RDEs) have gained attention as a promising technology for future aviation engines. However, the numerical studies of these systems pose severe challenges due to the broad range of spatial and temporal scales. In this study, we use an adaptive mesh refinement based compressible, reactive solver PeleC to resolve the broad range of scales and accurately capture shock and detonation waves using high-resolution numerical schemes. Multi- species transport along with compressible Navier-Stokes equations are solved in the model along with a finite-rate based chemistry model. Embedded boundary method is used to model the complex geometry consisting of discrete fuel nozzles and the combustion chamber. The fuel consisting predominantly of hydrogen is doped with varying levels of methane while air is used as the oxidizer. For a specified total pressure and temperature, the number of stable detonation waves is found to decrease with increasing methane concentration in the fuel mixture. Additionally, no stable detonation solutions are observed for methane composition higher than 20% by volume for the range of operating conditions studied (300-900K, 10 Atm). The increased presence of high temperature zones is also indicative of higher thermal NOx emissions at low methane concentrations. The effect of fuel-air mixture composition and temperature on the detonability, detonation wave structure, mode transitions and their stability are analyzed in this study in addition to their implication on NOx emission.

automatic mesh refinement↗
DOE OSTI2020

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↗