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

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 frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org
 .

/pdf/open-babel-an-open-chemical-toolbox-2c5goscrz3.pdf

Open Babel: An open chemical toolbox

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

We propose a model for collisions between particles of a granular material and calculate the restitution coefficients for the normal and tangential motion as functions of the impact velocity from considerations of dissipative viscoelastic collisions. Existing models of impact with dissipation as well as the classical Hertz impact theory are included in the present model as special cases. We find that the type of collision (smooth, reflecting or sticky) is determined by the impact velocity and by the surface properties of the colliding grains. We observe a rather nontrivial dependence of the tangential restitution coefficient on the impact velocity. \textcopyright{} 1996 The American Physical Society.

/pdf/model-for-collisions-in-granular-gases-30o51d5xir.pdf

Model for collisions in granular gases

Molecular Dynamics.- Event-Driven Molecular Dynamics.- Direct Simulation Monte Carlo.- Rigid-Body Dynamics.- Cellular Automata.- Bottom-to-Top Reconstruction.- Brownian Dynamics for the Simulation of Granular Flows.

/pdf/computational-granular-dynamics-models-and-algorithms-14bn9du5dw.pdf

Computational Granular Dynamics: Models and Algorithms

I MECHANICS OF PARTICLE COLLISIONS II GRANULAR GASES - VELOCITY DISTRIBUTION FUNCTION III SINGLE-PARTICLE TRANSPORT, SELF-DIFFUSION AND BROWNIAN MOTION IV TRANSPORT PROCESSES AND KINETIC COEFFICIENTS V STRUCTURE FORMATION

/pdf/kinetic-theory-of-granular-gases-11hrtne6me.pdf

Kinetic Theory of Granular Gases

We perform a dimension analysis for colliding viscoelastic spheres to show that the coefficient of normal restitution epsilon depends on the impact velocity g as epsilon=1-gamma(1)g(1/5)+gamma(2)g(2/5)-/+..., in accordance with recent findings. We develop a simple theory to find explicit expressions for coefficients gamma(1) and gamma(2). Using these and few next expansion coefficients for epsilon(g) we construct a Pade approximation for this function which may be used for a wide range of impact velocities where the concept of the viscoelastic collision is valid. The obtained expression reproduces quite accurately the existing experimental dependence epsilon(g) for ice particles.

Coefficient of restitution of colliding viscoelastic spheres.

http://www.mss.cbi.fau.de/content/uploads/parteli_particle_based_2015.pdf

Thorsten Pöschel

Papers

Model for collisions in granular gases

Computational Granular Dynamics: Models and Algorithms

Kinetic Theory of Granular Gases

Coefficient of restitution of colliding viscoelastic spheres.

Particle-based simulation of powder application in additive manufacturing