LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Changes in portlandite morphology with solvent composition: Atomistic simulations and experiment

Chemical compositions of improved model asphalt systems for molecular simulations

Using extensive molecular dynamics simulations of an equilibrium, glass-forming Lennard-Jones mixture, we characterize in detail the local atomic motions. We show that spatial correlations exist among particles undergoing extremely large (``mobile'') or extremely small (``immobile'') displacements over a suitably chosen time interval. The immobile particles form the cores of relatively compact clusters, while the mobile particles move cooperatively and form quasi-one-dimensional, stringlike clusters. The strength and length scale of the correlations between mobile particles are found to grow strongly with decreasing temperature, and the mean cluster size appears to diverge near the mode-coupling critical temperature. We show that these correlations in the particle displacements are related to equilibrium fluctuations in the local potential energy and local composition.

http://glotzerlab.engin.umich.edu/home/publications-pdfs/2000earlier/1999-PhysRevE.60.3107.pdf

Spatial correlations of mobility and immobility in a glass-forming Lennard-Jones liquid

Application performance is determined by a combination of many choices: hardware platform, runtime environment, languages and compilers used, algorithm choice and implementation, and more. In this complicated environment, we find that the use of mini-applications - small self-contained proxies for real applications - is an excellent approach for rapidly exploring the parameter space of all these choices. Furthermore, use of mini-applications enriches the interaction between application, library and computer system developers by providing explicit functioning software and concrete performance results that lead to detailed, focused discussions of design trade-offs, algorithm choices and runtime performance issues. In this paper we discuss a collection of mini-applications and demonstrate how we use them to analyze and improve application performance on new and future computer platforms.

/pdf/improving-performance-via-mini-applications-141kz27nto.pdf

Improving Performance via Mini-applications

The parallel implementation of a molecular dynamics code suitable for simulationof general molecular systems using spatial{decomposition methods is discussed. Long-range Coulombic forces are computed using a particle-mesh Ewald (PPPM) technique. A multiple{timescale integration method known as rRESPA is also used to improve the computational eeciency. The load{balancing and interprocessor communication issues that arise from implementing PPPM and rRESPA within a spatial{decomposition framework are highlighted. Some performance numbers for large{scale biomembrane simulations on a Intel Paragon are given.

Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations.

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Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations.