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

The discrete self-trapping equation

Multimillion-atom molecular-dynamics simulations are used to investigate the shock-induced phase transformation of solid iron. Above a critical shock strength, many small close-packed grains nucleate in the shock-compressed body-centered cubic crystal growing on a picosecond time scale to form larger, energetically favored grains. A split two-wave shock structure is observed immediately above this threshold, with an elastic precursor ahead of the lagging transformation wave. For even higher shock strengths, a single, overdriven wave is obtained. The dynamics and orientation of the developing close-packed grains depend on the shock strength and especially on the crystallographic shock direction. Orientational relations between the unshocked and shocked regions are similar to those found for the temperature-driven martensitic transformation in iron and its alloys.

http://www.thp.uni-due.de/~kai/science.pdf

Microscopic View of Structural Phase Transitions Induced by Shock Waves

Nonequilibrium molecular-dynamics simulations of shock waves in three-dimensional 10-million atom face-centered cubic crystals with cross-sectional dimensions of 100 by 100 unit cells show that the system slips along all of the available {111} slip planes, in different places along the nonplanar shock front. Comparison of these simulations with earlier ones on a smaller scale not only eliminates the possibility that the observed slippage is an artifact of transverse periodic boundary conditions, but also reveals the richness of the nanostructure left behind. By introducing a piston face that is no longer perfectly flat, mimicking a line or surface inhomogeneity in the unshocked material, it is shown that for weaker shock waves (below the perfect-crystal yield strength), stacking faults can be nucleated by preexisting extended defects.

https://science.sciencemag.org/content/sci/280/5372/2085.full.pdf

Plasticity Induced by Shock Waves in Nonequilibrium Molecular-Dynamics Simulations

In-situ x-ray diffraction studies of iron under shock conditions confirm unambiguously a phase change from the bcc ({alpha}) to hcp ({var_epsilon}) structure. Previous identification of this transition in shock-loaded iron has been inferred from the correlation between shock wave-profile analyses and static high-pressure x-ray measurements. This correlation is intrinsically limited because dynamic loading can markedly affect the structural modifications of solids. The in-situ measurements are consistent with a uniaxial collapse along the [001] direction and shuffling of alternate (110) planes of atoms, and in good agreement with large-scale non-equilibrium molecular dynamics simulations.

/pdf/direct-observation-of-the-alpha-epsilon-transition-in-shock-1dz1mp87ci.pdf

Direct Observation of the alpha-epsilon Transition in Shock-compressed Iron via Nanosecond X-ray Diffraction

The theory of self-trapping of amide I vibrational energy in crystalline acetanilide is studied in detail. A spectrum of stationary, self-trapped (soliton) solutions is determined and tested for dynamic stability. Only those solutions for which the amide I energy is concentrated near a single molecule were found to be stable. Exciton modes were found to be unstable to decay into solitons.

Peter S. Lomdahl

Papers

The discrete self-trapping equation

Microscopic View of Structural Phase Transitions Induced by Shock Waves

Plasticity Induced by Shock Waves in Nonequilibrium Molecular-Dynamics Simulations

Direct Observation of the alpha-epsilon Transition in Shock-compressed Iron via Nanosecond X-ray Diffraction

Soliton structure in crystalline acetanilide