https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

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.

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

/pdf/pattern-formation-outside-of-equilibrium-1601b9znum.pdf

Pattern formation outside of equilibrium

Mechanical properties of nanocrystalline materials

We have used x-ray diffraction with subnanosecond temporal resolution to measure the lattice parameters of orthogonal planes in shock compressed single crystals of silicon (Si) and copper (Cu). Despite uniaxial compression along the (400) direction of Si reducing the lattice spacing by nearly 11%, no observable changes occur in planes with normals orthogonal to the shock propagation direction. In contrast, shocked Cu shows prompt hydrostaticlike compression. These results are consistent with simple estimates of plastic strain rates based on dislocation velocity data. Although the response of materials to uniaxial shock compression has been a field of study for more than a century, our understanding at the lattice level of the response of crystals to rapid loading is still far from complete. While constitutive models are useful, a full description of phenomena such as shock-induced elastic-plastic flow and polymorphic phase transitions requires a knowledge of the atomic positions and the history of their rearrangement during the passage of the shock wave. In principle, one of the most direct methods of obtaining such information is the technique of in situ time-resolved x-ray diffraction (TXRD). Indeed, the TXRD experiments of Johnson and co-workers over three decades ago gave the first direct evidence of the retention of crystallinity under shock compression [1,2]. TXRD yields information about the interatomic spacings within the crystal. The change in Bragg angle due to the shock-induced alteration of the lattice parameter for monochromatic radiation is given, for small compressions, by simple differentiation of Bragg’s law: D2dhkl2dhkl 2 cotubDu. TXRD also provides information about the degree of plastic flow within the crystal: in the limit of purely hydrostatic response, an initially cubic lattice remains cubic under shock compression (at least in the hard sphere approximation). Thus diffraction from planes with reciprocal lattice vectors orthogonal to the shock propagation direction also exhibits angular shifts: a feature that has been confirmed by TXRD for certain crystals such as LiF and KCl under sufficiently intense loading [3‐5]. We provide here similar evidence for shocked single-crystal copper, which responds approximately hydrostatically to shocks of order 180 kbar on nanosecond time scales. However, plastic flow relies on dislocation generation and transport, a process that takes a characteristic time

http://www.meyersgroup.ucsd.edu/papers/journals/Meyers%20242.pdf

Anomalous elastic response of silicon to uniaxial shock compression on nanosecond time scales.

Parallel Algorithms for Short-range Molecular Dynamics

As computational power is increasing, molecular dynamics simulations are becoming more important in materials science, chemistry, physics, and other fields of science. We demonstrate weak and strong scaling of our classical molecular dynamics code SPaSM on Livermore's BlueGene/L architecture containing 131 072 IBM PowerPC440 processors. A maximum of 320 billion atoms have been simulated in double precision, corresponding to a cubic piece of solid copper with an edge length of 1.56 μm.

/pdf/molecular-dynamics-comes-of-age-320-billion-atom-simulation-2thtdm9dsm.pdf

MOLECULAR DYNAMICS COMES OF AGE: 320 BILLION ATOM SIMULATION ON BlueGene/L

From large-scale molecular-dynamics simulations of dynamic crack propagation, we find that cracks accelerate quickly to a relatively steady velocity. Energy released by bond breaking accumulates in a local phonon field that moves with the crack tip and promotes the emission of dislocations. Branching follows dislocation emission along a slip plane. The branching instability requires the crack to achieve a critical velocity, as well as in induction time for energy buildup at the crack tip. {copyright} {ital 1996 The American Physical Society.}

Dynamic crack processes via molecular dynamics

The dynamics of trans-polyacetylene is studied within the adiabatic model of Su, Schrieffer, and Heeger. A single soliton has a maximum velocity, ${v}_{m}$, which can be higher than the sound velocity. A long-time simulation shows that, from an initial electron-hole pair, a soliton and antisoliton emerge with velocities $\ifmmode\pm\else\textpm\fi{}{v}_{m}$ and that a persistent breather is left behind. This breather may account for the high-energy intragap structure observed in photoinduced absorption, including isotope dependence.

Peter S. Lomdahl

Papers

Anomalous elastic response of silicon to uniaxial shock compression on nanosecond time scales.

Parallel Algorithms for Short-range Molecular Dynamics

MOLECULAR DYNAMICS COMES OF AGE: 320 BILLION ATOM SIMULATION ON BlueGene/L

Dynamic crack processes via molecular dynamics

Breathers and Photoinduced Absorption in Polyacetylene