Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Quantum mechanics

Many-particle charged-particle plasma simulations using spatial meshes for the electromagnetic field solutions, particle-in-cell (PIC) merged with Monte Carlo collision (MCC) calculations, are coming into wide use for application to partially ionized gases. The author emphasizes the development of PIC computer experiments since the 1950s starting with one-dimensional (1-D) charged-sheet models, the addition of the mesh, and fast direct Poisson equation solvers for 2-D and 3-D. Details are provided for adding the collisions between the charged particles and neutral atoms. The result is many-particle simulations with many of the features met in low-temperature collision plasmas; for example, with applications to plasma-assisted materials processing, but also related to warmer plasmas at the edges of magnetized fusion plasmas. >

Particle-in-Cell Charged Particle Simulations, plus Monte Carlo Collisions with Neutral Atoms, PIC-MCC

Supernova theory, numerical and analytic, has made remarkable progress in the past decade. This progress was made possible by more sophisticated simulation tools, especially for neutrino transport, improved microphysics, and deeper insights into the role of hydrodynamic instabilities. Violent, large-scale nonradial mass motions are generic in supernova cores. The neutrino-heating mechanism, aided by nonradial flows, drives explosions, albeit low-energy ones, of O-Ne-Mg-core and some Fe-core progenitors. The characteristics of the neutrino emission from newborn neutron stars were revised, new features of the gravitational-wave signals were discovered, our notion of supernova nucleosynthesis was shattered, and our understanding of pulsar kicks and explosion asymmetries was significantly improved. But simulations also suggest that neutrino-powered explosions might not explain the most energetic supernovae and hypernovae, which seem to demand magnetorotational driving. Now that modeling is being advanced from...

https://www.annualreviews.org/doi/pdf/10.1146/annurev-nucl-102711-094901

Explosion Mechanisms of Core-Collapse Supernovae

Fluid dynamic turbulence is one of the most challenging computational physics problems because of the extremely wide range of time and space scales involved, the strong nonlinearity of the governing equations, and the many practical and important applications. While most linear fluid instabilities are well understood, the nonlinear interactions among them makes even the relatively simple limit of homogeneous isotropic turbulence difficult to treat physically, mathematically, and computationally. Turbulence is modeled computationally by a two-stage bootstrap process. The first stage, direct numerical simulation, attempts to resolve the relevant physical time and space scales but its application is limited to diffusive flows with a relatively small Reynolds number (Re). Using direct numerical simulation to provide a database, in turn, allows calibration of phenomenological turbulence models for engineering applications. Large eddy simulation incorporates a form of turbulence modeling applicable when the large-scale flows of interest are intrinsically time dependent, thus throwing common statistical models into question. A promising approach to large eddy simulation involves the use of high-resolution monotone computational fluid dynamics algorithms such as flux-corrected transport or the piecewise parabolic method which have intrinsic subgrid turbulence models coupled naturally to the resolved scales in the computed flow. The physical considerations underlying and evidence supporting this monotone integrated large eddy simulation approach are discussed.

New insights into large eddy simulation

We have numerically studied the instability of the spherically symmetric standing accretion shock wave against non-spherical perturbations. We have in mind the application to the collapse-driven supernovae in the post bounce phase, where the prompt shock wave generated by core bounce is commonly stalled. We take an experimental stand point in this paper. Using spherically symmetric, completely steady, shocked accretion flows as unperturbed states, we have clearly observed both the linear growth and the subsequent nonlinear saturation of the instability. In so doing, we have employed a realistic equation of state together with heating and cooling via neutrino reactions with nucleons. We have done a mode analysis based on the spherical harmonics decomposition and found that the modes with l=1, 2 are dominant not only in the linear regime, but also after the nonlinear couplings generate various modes and the saturation occurs. Varying the neutrino luminosity, we have constructed the unperturbed states both with and without a negative entropy-gradient. We have found that in both cases the growth of the instability is similar, suggesting the convection does not play a dominant role, which also appears to be supported by the recent linear analysis of the convection in accretion flows by Foglizzo et al. The real part of the eigen frequency seems to be mainly determined by the advection time rather than by the sound-crossing time. Whatever the cause may be, the instability is favorable for the shock revival.

Numerical Analysis on Standing Accretion Shock Instability with Neutrino Heating in the Supernova Cores

We have numerically studied the instability of the spherically symmetric standing accretion shock wave against nonspherical perturbations. We have in mind the application to collapse-driven supernovae in the postbounce phase, where the prompt shock wave generated by core bounce is commonly stalled. We take an experimental standpoint in this paper. Using spherically symmetric, completely steady, shocked accretion flows as unperturbed states, we have clearly observed both the linear growth and the subsequent nonlinear saturation of the instability. In so doing, we have employed a realistic equation of state, together with heating and cooling via neutrino reactions with nucleons. We have performed a mode analysis based on the spherical harmonics decomposition and found that the modes with l = 1,2 are dominant not only in the linear regime but also after nonlinear couplings generate various modes and saturation occurs. By varying the neutrino luminosity, we have constructed unperturbed states both with and without a negative entropy gradient. We have found that in both cases the growth of the instability is similar, suggesting that convection does not play a dominant role, which also appears to be supported by the recent linear analysis of the convection in accretion flows by Foglizzo et al. The oscillation period of the unstable l = 1 mode is found to fit better with the advection time rather than with the sound crossing time. Whatever the cause may be, the instability favors a shock revival.

http://iopscience.iop.org/article/10.1086/500554/pdf

Numerical analysis of standing accretion shock instability with neutrino heating in supernova cores

We have studied nonaxisymmetric standing accretion shock instabilities, or SASI, using three-dimensional (3D) hydrodynamical simulations. This is an extension of our previous study of axisymmetric SASI. We have prepared a spherically symmetric and steady accretion flow through a standing shock wave onto a proto-neutron star, taking into account a realistic equation of state and neutrino heating and cooling. This unperturbed model is meant to represent approximately the typical postbounce phase of core-collapse supernovae. We then added a small perturbation (~1%) to the radial velocity and computed the ensuing evolutions. Both axisymmetric and nonaxisymmetric perturbations have been imposed. We have applied mode analysis to the nonspherical deformation of the shock surface, using spherical harmonics. We have found that (1) the growth rates of SASI are degenerate with respect to the azimuthal index m of the spherical harmonics Ylm, just as expected for a spherically symmetric background; (2) nonlinear mode couplings produce only m = 0 modes for axisymmetric perturbations, whereas m≠ 0 modes are also generated in the nonaxisymmetric cases, according to the selection rule for quadratic couplings; (3) the nonlinear saturation level of each mode is lower in general for 3D than for 2D, because a larger number of modes contribute to turbulence in 3D; (4) low-l modes are dominant in the nonlinear phase; (5) equipartition is nearly established among different m modes in the nonlinear phase; (6) spectra with respect to l obey power laws with a slope slightly steeper for 3D; and (7) although these features are common to the models with and without a shock revival at the end of the simulation, the dominance of low- l modes is more remarkable in the models with a shock revival.

https://iopscience.iop.org/article/10.1086/533582/pdf

Three-dimensional simulations of standing accretion shock instability in core-collapse supernovae

We study the effects of rotation on standing accretion shock instability (SASI) by performing three-dimensional hydrodynamics simulations. Taking into account a realistic equation of state and neutrino heating/cooling, we prepare a spherically symmetric and steady accretion flow through a standing shock wave onto a proto-neutron star (PNS). When the SASI enters the nonlinear phase, we impose uniform rotation on the flow advecting from the outer boundary of the iron core, whose specific angular momentum is assumed to agree with recent stellar evolution models. Using spherical harmonics in space and Fourier decompositions in time, we perform mode analysis of the nonspherical deformed shock wave to observe rotational effects on the SASI in the nonlinear phase. We find that rotation imposed on the axisymmetric flow does not make any spiral modes and hardly affects sloshing modes, except for steady l = 2, m = 0 modes. In contrast, rotation imposed on the nonaxisymmetric flow increases the amplitude of spiral modes so that some spiral flows accreting on the PNS are more clearly formed inside the shock wave than without rotation. The amplitudes of spiral modes increase significantly with rotation in the progressive direction.

http://iopscience.iop.org/article/10.1088/0004-637X/700/1/232/pdf

Effects of rotation on standing accretion shock instability in nonlinear phase for core-collapse supernovae

We study the properties of gravitational waves (GWs) based on three-dimensional (3D) simulations, which demonstrate neutrino-driven explosions aided by standing accretion shock instability (SASI). Pushed by evidence supporting slow rotation prior to core collapse, we focus on the asphericities in neutrino emissions and matter motions outside the protoneutron star. By performing a ray-tracing calculation in 3D, we estimate accurately the gravitational waveforms from anisotropic neutrino emissions. In contrast to the previous work assuming axisymmetry, we find that the gravitational waveforms vary much more stochastically because the explosion anisotropies depend sensitively on the growth of SASI which develops chaotically in all directions. Our results show that the GW spectrum has its peak near ~100 Hz, reflecting SASI-induced matter overturns of ~O(10) ms. We point out that the detection of such signals, possibly visible to the LIGO-class detectors for a Galactic supernova, could be an important probe into the long-veiled explosion mechanism.

Naofumi Ohnishi

Papers

Numerical Analysis on Standing Accretion Shock Instability with Neutrino Heating in the Supernova Cores

Numerical analysis of standing accretion shock instability with neutrino heating in supernova cores

Three-dimensional simulations of standing accretion shock instability in core-collapse supernovae

Effects of rotation on standing accretion shock instability in nonlinear phase for core-collapse supernovae

Stochastic nature of gravitational waves from supernova explosions with standing accretion shock instability