arXiv subjects

Jeffrey S. Oishi

Publications and source records attributed to Jeffrey S. Oishi.

At least 37 records · Page 2Linked to original sources

arXiv2018

Accelerated evolution of convective simulations

High Peclet number, turbulent convection is a classic system with a large timescale separation between flow speeds and the thermal relaxation time. In this paper, we present a method of fast-forwarding through the long thermal relaxation of convective simulations, and we test the validity of this method. This accelerated evolution (AE) method involves measuring the dynamics of convection early in a simulation and using its characteristics to adjust the mean thermodynamic profile within the domain towards its evolved state. We study Rayleigh-Bénard convection as a test case for AE. Evolved flow properties of AE solutions are measured to be within a few percent of solutions which are reached through standard evolution (SE) over a full thermal timescale. At the highest values of the Rayleigh number at which we compare SE and AE, we find that AE solutions require roughly an order of magnitude fewer computing hours to evolve than SE solutions.

physics.flu-dyn↗

arXiv2018

Tensor calculus in spherical coordinates using Jacobi polynomials, Part-II: Implementation and Examples

We present a simulation code which can solve broad ranges of partial differential equations in a full sphere. The code expands tensorial variables in a spectral series of spin-weighted spherical harmonics in the angular directions and a scaled Jacobi polynomial basis in the radial direction, as described in Part-I. Nonlinear terms are calculated by transforming from the coefficients in the spectral series to the value of each quantity on the physical grid, where it is easy to calculate products and perform other local operations. The expansion makes it straightforward to solve equations in tensor form (i.e., without decomposition into scalars). We propose and study several unit tests which demonstrate the code can accurately solve linear problems, implement boundary conditions, and transform between spectral and physical space. We then run a series of benchmark problems proposed in Marti et al (2014), implementing the hydrodynamic and magnetohydrodynamic equations. We are able to calculate more accurate solutions than reported in Marti et al 2014 by running at higher spatial resolution and using a higher-order timestepping scheme. We find the rotating convection and convective dynamo benchmark problems depend sensitively on details of timestepping and data analysis. We also demonstrate that in low resolution simulations of the dynamo problem, small changes in a numerical scheme can lead to large changes in the solution. To aid future comparison to these benchmarks, we include the source code used to generate the data, as well as the data and analysis scripts used to generate the figures.

astro-ph.IM↗

arXiv2018

Convective dynamics and disequilibrium chemistry in the atmospheres of giant planets and brown dwarfs

Disequilibrium chemical processes have a large effect upon the spectra of substellar objects. To study these effects, dynamical disequilibrium has been parameterized using the quench and eddy diffusion approximations, but little work has been done to explore how these approximations perform under realistic planetary conditions in different dynamical regimes. As a first step in addressing this problem, we study the localized, small scale convective dynamics of planetary atmospheres by direct numerical simulation of fully compressible hydrodynamics with reactive tracers using the Dedalus code. Using polytropically-stratified, plane parallel atmospheres in 2- and 3-D, we explore the quenching behavior of different abstract chemical species as a function of the dynamical conditions of the atmosphere as parameterized by the Rayleigh number. We find that in both 2- and 3-D, chemical species quench deeper than would be predicted based on simple mixing length arguments. Instead, it is necessary to employ length scales based on the chemical equilibrium profile of the reacting species in order to predict quench points and perform chemical kinetics modeling in 1-D. Based on the results of our simulations, we provide a new length scale, derived from the chemical scale height, which can be used to perform these calculations. This length scale is simple to calculate from known chemical data and makes reasonable predictions for our dynamical simulations.

astro-ph.EP↗

arXiv2018

Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project

As the Science Mission Directorate contemplates establishing an open code policy, we consider it timely to share our experiences as the developers of the open-source partial differential equation solver Dedalus. Dedalus is a flexible framework for solving partial differential equations. Its development team primarily uses it for studying stellar and planetary astrophysics. Dedalus was developed originally for astrophysical fluid dynamics (AFD), though it has found a much broader user base, including applied mathematicians, plasma physicists, and oceanographers. Here, we will focus on issues related to open-source software from the perspective of AFD. We use the term AFD with the understanding that astrophysics simulations are inherently multi-physics: fluid dynamics coupled with some combination of gravitational dynamics, radiation transfer, relativity, and magnetic fields. In practice, a few well-known open-source simulation packages represent a large fraction of published work in the field. However, we will argue that an open-code policy should encompass not just these large simulation codes, but also the input files and analysis scripts. It is our interest that NASA adopt an open-code policy because without it, reproducibility in computational science is needlessly hampered.

astro-ph.IM↗

arXiv2017

The weakly nonlinear magnetorotational instability in a local geometry

The magnetorotational instability (MRI) is a fundamental process of accretion disk physics, but its saturation mechanism remains poorly understood despite considerable theoretical and computational effort. We present a multiple scales analysis of the non-ideal MRI in the weakly nonlinear regime -- that is, when the most unstable MRI mode has a growth rate asymptotically approaching zero from above. Here, we develop our theory in a local, Cartesian channel. Our results confirm the finding by Umurhan et al. (2007) that the perturbation amplitude follows a Ginzburg-Landau equation. We further find that the Ginzburg-Landau equation will arise for the local MRI system with shear-periodic boundary conditions when the effects of ambipolar diffusion are considered. A detailed force balance for the saturated azimuthal velocity and vertical magnetic field demonstrates that even when diffusive effects are important, the bulk flow saturates via the combined processes of reducing the background shear and rearranging and strengthening the background vertical magnetic field. We directly simulate the Ginzburg-Landau amplitude evolution for our system and demonstrate the pattern formation our model predicts on long length and time scales. We compare the weakly nonlinear theory results to a direct numerical simulation of the MRI in a thin-gap Taylor Couette flow.

astro-ph.HE↗

arXiv2017

The weakly nonlinear magnetorotational instability in a global, cylindrical Taylor-Couette flow

We conduct a global, weakly nonlinear analysis of the magnetorotational instability (MRI) in a Taylor-Couette flow. This is a multiscale perturbative treatment of the nonideal, axisymmetric MRI near threshold, subject to realistic radial boundary conditions and cylindrical geometry. We analyze both the standard MRI, initialized by a constant vertical background magnetic field, and the helical MRI, with an azimuthal background field component. This is the first weakly nonlinear analysis of the MRI in a global Taylor-Couette geometry, as well as the first weakly nonlinear analysis of the helical MRI. We find that the evolution of the amplitude of the standard MRI is described by a real Ginzburg-Landau equation (GLE), while the amplitude of the helical MRI takes the form of a complex GLE. This suggests that the saturated state of the helical MRI may itself be unstable on long spatial and temporal scales.

astro-ph.HE↗

arXiv2016

Turbulent Chemical Diffusion in Convectively Bounded Carbon Flames

It has been proposed that mixing induced by convective overshoot can disrupt the inward propagation of carbon deflagrations in super-asymptotic giant branch stars. To test this theory, we study an idealized model of convectively bounded carbon flames with 3D hydrodynamic simulations of the Boussinesq equations using the pseudospectral code Dedalus. Because the flame propagation timescale is much longer than the convection timescale, we approximate the flame as fixed in space, and only consider its effects on the buoyancy of the fluid. By evolving a passive scalar field, we derive a {\it turbulent} chemical diffusivity produced by the convection as a function of height, $D_{\rm t}(z)$. Convection can stall a flame if the chemical mixing timescale, set by the turbulent chemical diffusivity, $D_{\rm t}$, is shorter than the flame propagation timescale, set by the thermal diffusivity, $κ$, i.e., when $D_{\rm t}>κ$. However, we find $D_{\rm t}<κ$ for most of the flame because convective plumes are not dense enough to penetrate into the flame. Extrapolating to realistic stellar conditions, this implies that convective mixing cannot stall a carbon flame and that "hybrid carbon-oxygen-neon" white dwarfs are not a typical product of stellar evolution.

astro-ph.SR↗

arXiv2016

Tensor calculus in polar coordinates using Jacobi polynomials

Spectral methods are an efficient way to solve partial differential equations on domains possessing certain symmetries. The utility of a method depends strongly on the choice of spectral basis. In this paper we describe a set of bases built out of Jacobi polynomials, and associated operators for solving scalar, vector, and tensor partial differential equations in polar coordinates on a unit disk. By construction, the bases satisfy regularity conditions at r=0 for any tensorial field. The coordinate singularity in a disk is a prototypical case for many coordinate singularities. The work presented here extends to other geometries. The operators represent covariant derivatives, multiplication by azimuthally symmetric functions, and the tensorial relationship between fields. These arise naturally from relations between classical orthogonal polynomials, and form a Heisenberg algebra. Other past work uses more specific polynomial bases for solving equations in polar coordinates. The main innovation in this paper is to use a larger set of possible bases to achieve maximum bandedness of linear operations. We provide a series of applications of the methods, illustrating their ease-of-use and accuracy.

math.NA↗

arXiv2016

Hybrid Adaptive Ray-Moment Method (HARM$^2$): A Highly Parallel Method for Radiation Hydrodynamics on Adaptive Grids

We present a highly-parallel multi-frequency hybrid radiation hydrodynamics algorithm that combines a spatially-adaptive long characteristics method for the radiation field from point sources with a moment method that handles the diffuse radiation field produced by a volume-filling fluid. Our Hybrid Adaptive Ray-Moment Method (HARM$^2$) operates on patch-based adaptive grids, is compatible with asynchronous time stepping, and works with any moment method. In comparison to previous long characteristics methods, we have greatly improved the parallel performance of the adaptive long-characteristics method by developing a new completely asynchronous and non-blocking communication algorithm. As a result of this improvement, our implementation achieves near-perfect scaling up to $\mathcal{O}(10^3)$ processors on distributed memory machines. We present a series of tests to demonstrate the accuracy and performance of the method.

astro-ph.IM↗

arXiv2015

Numerical Simulations of Internal Wave Generation by Convection in Water

Water's density maximum at 4C makes it well suited to study internal gravity wave excitation by convection: an increasing temperature profile is unstable to convection below 4C, but stably stratified above 4C. We present numerical simulations of a water-like fluid near its density maximum in a two dimensional domain. We successfully model the damping of waves in the simulations using linear theory, provided we do not take the weak damping limit typically used in the literature. In order to isolate the physical mechanism exciting internal waves, we use the novel spectral code Dedalus to run several simplified model simulations of our more detailed simulation. We use data from the full simulation as source terms in two simplified models of internal wave excitation by convection: bulk excitation by convective Reynolds stresses, and interface forcing via the mechanical oscillator effect. We find excellent agreement between the waves generated in the full simulation and the simplified simulation implementing the bulk excitation mechanism. The interface forcing simulations over excite high frequency waves because they assume the excitation is by the "impulsive" penetration of plumes, which spreads energy to high frequencies. However, we find the real excitation is instead by the "sweeping" motion of plumes parallel to the interface. Our results imply that the bulk excitation mechanism is a very accurate heuristic for internal wave generation by convection.

astro-ph.SR↗

arXiv2015

Self-generated turbulence in magnetic reconnection

Classical Sweet-Parker models of reconnection predict that reconnection rates depend inversely on the resistivity, usually parameterized using the dimensionless Lundquist number ($\Lund$). We describe magnetohydrodynamic (MHD) simulations using a static, nested grid that show the development of a three-dimensional instability in the plane of a current sheet between reversing field lines without a guide field. The instability leads to rapid reconnection of magnetic field lines at a rate independent of $\Lund$ over at least the range $3.2\times 10^3 \lesssim \Lund \lesssim 3.2 \times 10^5$ resolved by the simulations. We find that this instability occurs even for cases with $\Lund \lesssim 10^4$ that in our models appear stable to the recently described, two-dimensional, plasmoid instability. Our results suggest that three-dimensional, MHD processes alone produce fast (resistivity independent) reconnection without recourse to kinetic effects or external turbulence. The unstable reconnection layers provide a self-consistent environment in which the extensively studied turbulent reconnection process can occur.

astro-ph.SR↗

arXiv2014

Radial Stresses and Energy Transport in Accretion Disks

Early in the study of viscous accretion disks it was realized that energy transfers from distant sources must be important, not least because the flow at the disk midplane in the bulk of the disk is likely outwards, out of the gravitational potential well. If the source of the viscosity is powered by accretion, such as in the case of the magneto-rotational instability, such distant energy sources must lie in the innermost regions of the disk, where accretion occurs even at the midplane. We argue here that modulations in this energy supply can alter the accretion rate on dynamical, rather than far longer viscous, time scales. This means that both the steady state value of and fluctuations in the inner disk's accretion rate, depending on the details of the inner boundary condition and occurring on the inner disk's rapid evolution time, can affect the outer disk. This is particularly interesting because observations have shown that disk accretion is not steady (e.g.~EX Lupi type objects). We also note that the power supplied to shearing boxes is set by the boxes themselves rather than the physical energy fluxes in a global disk. That is, their saturated magnetic field is not subject to the full set of energy constraints present in an actual disk. Our analysis suggests that large scale radial transport of energy has a critical impact on the evolution and variability of accretion disks.

astro-ph.EP↗

arXiv2014

Conduction in low Mach number flows: Part I Linear & weakly nonlinear regimes

Thermal conduction is an important energy transfer and damping mechanism in astrophysical flows. Fourier's law - the heat flux is proportional to the negative temperature gradient, leading to temperature diffusion - is a well-known empirical model of thermal conduction. However, entropy diffusion has emerged as an alternative thermal conduction model, despite not ensuring the monotonicity of entropy. This paper investigates the differences between temperature and entropy diffusion for both linear internal gravity waves and weakly nonlinear convection. In addition to simulating the two thermal conduction models with the fully compressible Navier-Stokes equations, we also study their effects in the reduced, "sound-proof" anelastic and pseudo-incompressible equations. We find that in the linear and weakly nonlinear regimes, temperature and entropy diffusion give quantitatively similar results, although there are some larger errors in the pseudo-incompressible equations with temperature diffusion due to inaccuracies in the equation of state. Extrapolating our weakly nonlinear results, we speculate that differences between temperature and entropy diffusion might become more important for strongly turbulent convection.

astro-ph.SR↗

arXiv2013

Enzo: An Adaptive Mesh Refinement Code for Astrophysics

This paper describes the open-source code Enzo, which uses block-structured adaptive mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in 1, 2, and 3 dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically-thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.

astro-ph.IM↗

arXiv2011

Magnetic Fields in Population III Star Formation

We study the buildup of magnetic fields during the formation of Population III star-forming regions, by conducting cosmological simulations from realistic initial conditions and varying the Jeans resolution. To investigate this in detail, we start simulations from identical initial conditions, mandating 16, 32 and 64 zones per Jeans length, and studied the variation in their magnetic field amplification. We find that, while compression results in some amplification, turbulent velocity fluctuations driven by the collapse can further amplify an initially weak seed field via dynamo action, provided there is sufficient numerical resolution to capture vortical motions (we find this requirement to be 64 zones per Jeans length, slightly larger than, but consistent with previous work run with more idealized collapse scenarios). We explore saturation of amplification of the magnetic field, which could potentially become dynamically important in subsequent, fully-resolved calculations. We have also identified a relatively surprising phenomena that is purely hydrodynamic: the higher-resolved simulations possess substantially different characteristics, including higher infall-velocity, increased temperatures inside 1000 AU, and decreased molecular hydrogen content in the innermost region. Furthermore, we find that disk formation is suppressed in higher-resolution calculations, at least at the times that we can follow the calculation. We discuss the effect this may have on the buildup of disks over the accretion history of the first clump to form as well as the potential for gravitational instabilities to develop and induce fragmentation.

astro-ph.CO↗

arXiv2011

Simulating the Common Envelope Phase of a Red Giant Using SPH and Uniform Grid Codes

We use three-dimensional hydrodynamical simulations to study the rapid infall phase of the common envelope interaction of a red giant branch star of mass equal to 0.88 \msun and a companion star of mass ranging from 0.9 down to 0.1 \msun. We first compare the results obtained using two different numerical techniques with different resolutions, and find overall very good agreement. We then compare the outcomes of those simulations with observed systems thought to have gone through a common envelope. The simulations fail to reproduce those systems in the sense that most of the envelope of the donor remains bound at the end of the simulations and the final orbital separations between the donor's remnant and the companion, ranging from 26.8 down to 5.9 \rsun, are larger than the ones observed. We suggest that this discrepancy vouches for recombination playing an essential role in the ejection of the envelope and/or significant shrinkage of the orbit happening in the subsequent phase.

astro-ph.SR↗

arXiv2011

Magnetorotational turbulence transports angular momentum in stratified disks with low magnetic Prandtl number but magnetic Reynolds number above a critical value

The magnetorotational instability (MRI) may dominate outward transport of angular momentum in accretion disks, allowing material to fall onto the central object. Previous work has established that the MRI can drive a mean-field dynamo, possibly leading to a self-sustaining accretion system. Recently, however, simulations of the scaling of the angular momentum transport parameter $\alphaSS$ with the magnetic Prandtl number $\Prandtl$ have cast doubt on the ability of the MRI to transport astrophysically relevant amounts of angular momentum in real disk systems. Here, we use simulations including explicit physical viscosity and resistivity to show that when vertical stratification is included, mean field dynamo action operates, driving the system to a configuration in which the magnetic field is not fully helical. This relaxes the constraints on the generated field provided by magnetic helicity conservation, allowing the generation of a mean field on timescales independent of the resistivity. Our models demonstrate the existence of a critical magnetic Reynolds number $\Rmagc$, below which transport becomes strongly $\Prandtl$-dependent and chaotic, but above which the transport is steady and $\Prandtl$-independent. Prior simulations showing $\Prandtl$-dependence had $\Rmag < \Rmagc$. We conjecture that this steady regime is possible because the mean field dynamo is not helicity-limited and thus does not depend on the details of the helicity ejection process. Scaling to realistic astrophysical parameters suggests that disks around both protostars and stellar mass black holes have $\Rmag >> \Rmagc$. Thus, we suggest that the strong $\Prandtl$ dependence seen in recent simulations does not occur in real systems.

astro-ph.SR↗

arXiv2010

A Multi-Code Analysis Toolkit for Astrophysical Simulation Data

The analysis of complex multiphysics astrophysical simulations presents a unique and rapidly growing set of challenges: reproducibility, parallelization, and vast increases in data size and complexity chief among them. In order to meet these challenges, and in order to open up new avenues for collaboration between users of multiple simulation platforms, we present yt (available at http://yt.enzotools.org/), an open source, community-developed astrophysical analysis and visualization toolkit. Analysis and visualization with yt are oriented around physically relevant quantities rather than quantities native to astrophysical simulation codes. While originally designed for handling Enzo's structure adaptive mesh refinement (AMR) data, yt has been extended to work with several different simulation methods and simulation codes including Orion, RAMSES, and FLASH. We report on its methods for reading, handling, and visualizing data, including projections, multivariate volume rendering, multi-dimensional histograms, halo finding, light cone generation and topologically-connected isocontour identification. Furthermore, we discuss the underlying algorithms yt uses for processing and visualizing data, and its mechanisms for parallelization of analysis tasks.

astro-ph.IM↗