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

to be done in this area. Face recognition is a problem that scarcely clamoured for attention before the computer age but, having surfaced, has involved a wide range of techniques and has attracted the attention of some fine minds (David Mumford was a Fields Medallist in 1974). This singular application of mathematical modelling to a messy applied problem of obvious utility and importance but with no unique solution is a pretty one to share with students: perhaps, returning to the source of our opening quotation, we may invert Duncan's earlier observation, 'There is an art to find the mind's construction in the face!'.

Linear and nonlinear waves, by G. B. Whitham. Pp.636. £50. 1999. ISBN 0 471 35942 4 (Wiley).

Physical Review B

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

A meshfree method based on the peridynamic model of solid mechanics

Some materials may naturally form discontinuities such as cracks as a result of deformation. As an aid to the modeling of such materials, a new framework for the basic equations of continuum mechanics, called the "peridynamic" formulation, is proposed. The propagation of linear stress waves in the new theory is discussed, and wave dispersion relations are derived. Material stability and its connection with wave propagation is investigated. It is demonstrated by an example that the reformulated approach permits the solution of fracture problems using the same equations either on or off the crack surface or crack tip. This is an advantage for modeling problems in which the location of a crack is not known in advance.

https://digital.library.unt.edu/ark:/67531/metadc664843/m2/1/high_res_d/1895.pdf

Reformulation of Elasticity Theory for Discontinuities and Long-Range Forces

A generalization of the original peridynamic framework for solid mechanics is proposed. This generalization permits the response of a material at a point to depend collectively on the deformation of all bonds connected to the point. This extends the types of material response that can be reproduced by peridynamic theory to include an explicit dependence on such collectively determined quantities as volume change or shear angle. To accomplish this generalization, a mathematical object called a deformation state is defined, a function that maps any bond onto its image under the deformation. A similar object called a force state is defined, which contains the forces within bonds of all lengths and orientation. The relation between the deformation state and force state is the constitutive model for the material. In addition to providing a more general capability for reproducing material response, the new framework provides a means to incorporate a constitutive model from the conventional theory of solid mechanics directly into a peridynamic model. It also allows the condition of plastic incompressibility to be enforced in a peridynamic material model for permanent deformation analogous to conventional plasticity theory.

/pdf/peridynamic-states-and-constitutive-modeling-2gjj1y6ke8.pdf

Peridynamic States and Constitutive Modeling

Publisher Summary The classical theory of solid mechanics is based on the assumption of a continuous distribution of mass within a body and all internal forces are contact forces that act across zero distance. The mathematical description of a solid that follows from these assumptions relies on PDEs that additionally assume sufficient smoothness of the deformation for the PDEs to make sense in their either strong or weak forms. The classical theory has been demonstrated to provide a good approximation to the response of real materials down to small length scales, particularly in single crystals, provided these assumptions are met. Nevertheless, technology increasingly involves the design and fabrication of devices at smaller and smaller length scales, even interatomic dimensions.

Stewart A. Silling

Papers

Reformulation of Elasticity Theory for Discontinuities and Long-Range Forces

A meshfree method based on the peridynamic model of solid mechanics

Peridynamic States and Constitutive Modeling

Peridynamic Theory of Solid Mechanics

Peridynamics via finite element analysis