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

The concept of self-organized criticality was introduced to explain the behaviour of the sandpile model. In this model, particles are randomly dropped onto a square grid of boxes. When a box accumulates four particles they are redistributed to the four adjacent boxes or lost off the edge of the grid. Redistributions can lead to further instabilities with the possibility of more particles being lost from the grid, contributing to the size of each ‘avalanche’. These model ‘avalanches’ satisfied a power-law frequency‐area distribution with a slope near unity. Other cellular-automata models, including the slider-block and forest-fire models, are also said to exhibit self-organized critical behaviour. It has been argued that earthquakes, landslides, forest fires, and species extinctions are examples of self-organized criticality in nature. In addition, wars and stock market crashes have been associated with this behaviour. The forest-fire model is particularly interesting in terms of its relation to the critical-point behaviour of the sitepercolation model. In the basic forest-fire model, trees are randomly planted on a grid of points. Periodically in time, sparks are randomly dropped on the grid. If a spark drops on a tree, that tree and adjacent trees burn in a model fire. The fires are the ‘avalanches’ and they are found to satisfy power-law frequency‐area distributions with slopes near unity. This forest-fire model is closely related to the site-percolation model, that exhibits critical behaviour. In the forest-fire model there is an inverse cascade of trees from small clusters to large clusters, trees are lost primarily from model fires that destroy the largest clusters. This quasi steady-state cascade gives a power-law frequency‐area distribution for both clusters of trees and smaller fires. The site-percolation model is equivalent to the forest-fire model without fires. In this case there is a transient cascade of trees from small to large clusters and a power-law distribution is found only at a critical density of trees.

/pdf/self-organized-criticality-4v87dkoa15.pdf

Self-organized criticality

Discrete particle simulation of particulate systems: A review of major applications and findings

It has been thought that sheets of cells move by traction forces exerted by the cells at the leading edge of the sheet. Using traction microscopy to create a map of physical forces, it is now shown that in fact it is cells many rows from the front that do most of the work. Fundamental biological processes including morphogenesis, tissue repair and tumour metastasis require collective cell motions1,2,3, and to drive these motions cells exert traction forces on their surroundings4. Current understanding emphasizes that these traction forces arise mainly in ‘leader cells’ at the front edge of the advancing cell sheet5,6,7,8,9. Our data are contrary to that assumption and show for the first time by direct measurement that traction forces driving collective cell migration arise predominately many cell rows behind the leading front edge and extend across enormous distances. Traction fluctuations are anomalous, moreover, exhibiting broad non-Gaussian distributions characterized by exponential tails10,11,12. Taken together, these unexpected findings demonstrate that although the leader cell may have a pivotal role in local cell guidance, physical forces that it generates are but a small part of a global tug-of-war involving cells well back from the leading edge.

/pdf/physical-forces-during-collective-cell-migration-3s53rslx6s.pdf

Physical forces during collective cell migration

Interparticle forces in granular media form an inhomogeneous distribution of filamentary force chains. Understanding such forces and their spatial correlations, specifically in response to forces at the system boundaries, represents a fundamental goal of granular mechanics. The problem is of relevance to civil engineering, geophysics and physics, being important for the understanding of jamming, shear-induced yielding and mechanical response. Here we report measurements of the normal and tangential grain-scale forces inside a two-dimensional system of photoelastic disks that are subject to pure shear and isotropic compression. Various statistical measures show the underlying differences between these two stress states. These differences appear in the distributions of normal forces (which are more rounded for compression than shear), although not in the distributions of tangential forces (which are exponential in both cases). Sheared systems show anisotropy in the distributions of both the contact network and the contact forces. Anisotropy also occurs in the spatial correlations of forces, which provide a quantitative replacement for the idea of force chains. Sheared systems have long-range correlations in the direction of force chains, whereas isotropically compressed systems have short-range correlations regardless of the direction.

Contact force measurements and stress-induced anisotropy in granular materials.

We study the origin of the scaling behavior in frictionless granular media above the jamming transition by analyzing their linear response. The response to local forcing is non-self-averaging and fluctuates over a length scale that diverges at the jamming transition. The response to global forcing becomes increasingly nonaffine near the jamming transition. This is due to the proximity of floppy modes, the influence of which we characterize by the local linear response. We show that the local response also governs the anomalous scaling of elastic constants and contact number.

/pdf/critical-scaling-in-linear-response-of-frictionless-granular-3mpqfgzq10.pdf

Critical scaling in linear response of frictionless granular packings near jamming.

Force networks form the skeleton of static granular matter. They are the key factor that determines mechanical properties such as stability, elasticity and sound transmission, which are important for civil engineering and industrial processing. Previous studies have focused on investigations of the global structure of external forces (the boundary condition) and on the probability distribution of individual contact forces. So far, however, precise knowledge of the disordered spatial structure of the force network has remained elusive. Here we report that molecular dynamics simulations of realistic granular packings reveal scale invariance of clusters of particles interacting by means of relatively strong forces. Despite visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, thereby determining a universality class. Unexpectedly, the flat ensemble of force configurations (a simple generalization of equilibrium statistical mechanics) belongs to this universality class, whereas some widely studied simplified models do not. This implies that the elasticity of the grains and their geometrical disorder do not affect the universal mechanical properties.

http://export.arxiv.org/pdf/cond-mat/0601047

Scale invariance and universality of force networks in static granular matter

We present numerical simulations of acoustic wave propagation in confined granular systems consisting of particles interacting with the three-dimensional Hertz-Mindlin force law. The response to a short mechanical excitation on one side of the system is found to be a propagating coherent wave front followed by random oscillations made of multiply scattered waves. We find that the coherent wave front is insensitive to details of the packing: force chains do not play an important role in determining this wave front. The coherent wave propagates linearly in time, and its amplitude and width depend as a power law on distance, while its velocity is roughly compatible with the predictions of macroscopic elasticity. As there is at present no theory for the broadening and decay of the coherent wave, we numerically and analytically study pulse propagation in a one-dimensional chain of identical elastic balls. The results for the broadening and decay exponents of this system differ significantly from those of the random packings. In all our simulations, the speed of the coherent wave front scales with pressure as p1/6; we compare this result with experimental data on various granular systems where deviations from the p1/6 behavior are seen. We briefly discuss the eigenmodes of the system and effects of damping are investigated as well.

/pdf/elastic-wave-propagation-in-confined-granular-systems-1iond2h4to.pdf

Elastic wave propagation in confined granular systems

We probe the nature of the jamming transition of frictional granular media by studying their vibrational properties as a function of the applied pressure p and friction coefficient μ. The density of vibrational states exhibits a crossover from a plateau at frequencies ω≳ω∗(p,μ) to a linear growth for ω≲ω∗(p,μ). We show that ω∗ is proportional to Δz, the excess number of contacts per grain relative to the minimally allowed, isostatic value. For zero and infinitely large friction, typical packings at the jamming threshold have Δz→0, and then exhibit critical scaling. We study the nature of the soft modes in these two limits, and find that the ratio of elastic moduli is governed by the distance from isostaticity.

/pdf/critical-and-noncritical-jamming-of-frictional-grains-4mwc9vrlig.pdf

Critical and noncritical jamming of frictional grains.

We report scanning tunneling microscopy observations, which imply that all atoms in a Cu(001) surface move frequently, even at room temperature. Using a low density of embedded indium ``tracer'' atoms, we visualize the diffusive motion of surface atoms. Surprisingly, the indium atoms seem to make concerted, long jumps. Responsible for this motion is an ultralow density of surface vacancies, diffusing rapidly within the surface. This interpretation is supported by a detailed analysis of the displacement distribution of the indium atoms, which reveals a shape characteristic for the vacancy mediated diffusion mechanism that we propose.

/pdf/nothing-moves-a-surface-vacancy-mediated-surface-diffusion-3khtz12qtg.pdf

Ellák Somfai

Papers

Critical scaling in linear response of frictionless granular packings near jamming.

Scale invariance and universality of force networks in static granular matter

Elastic wave propagation in confined granular systems

Critical and noncritical jamming of frictional grains.

Nothing Moves a Surface: Vacancy Mediated Surface Diffusion