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

Simulation and the monte carlo method

Summary
In this paper, we develop a dual-horizon peridynamics (DH-PD) formulation that naturally includes varying horizon sizes and completely solves the ‘ghost force’ issue Therefore, the concept of dual horizon is introduced to consider the unbalanced interactions between the particles with different horizon sizes The present formulation fulfills both the balances of linear momentum and angular momentum exactly Neither the ‘partial stress tensor’ nor the ‘slice’ technique is needed to ameliorate the ghost force issue We will show that the traditional peridynamics can be derived as a special case of the present DH-PD All three peridynamic formulations, namely, bond-based, ordinary state-based, and non-ordinary state-based peridynamics, can be implemented within the DH-PD framework Our DH-PD formulation allows for h-adaptivity and can be implemented in any existing peridynamics code with minimal changes A simple adaptive refinement procedure is proposed, reducing the computational cost Both two-dimensional and three-dimensional examples including the Kalthoff–Winkler experiment and plate with branching cracks are tested to demonstrate the capability of the method Copyright © 2016 John Wiley & Sons, Ltd

Dual‐horizon peridynamics

We present an open-source software framework called PERMIX for multiscale modeling and simulation of fracture in solids. The framework is an object oriented open-source effort written primarily in Fortran 2003 standard with Fortran/C++ interfaces to a number of other libraries such as LAMMPS, ABAQUS, LS-DYNA and GMSH. Fracture on the continuum level is modeled by the extended finite element method (XFEM). Using several novel or state of the art methods, the piece software handles semi-concurrent multiscale methods as well as concurrent multiscale methods for fracture, coupling two continuum domains or atomistic domains to continuum domains, respectively. The efficiency of our open-source software is shown through several simulations including a 3D crack modeling in clay nanocomposites, a semi-concurrent FE-FE coupling, a 3D Arlequin multiscale example and an MD-XFEM coupling for dynamic crack propagation.

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A computational library for multiscale modeling of material failure

A review of predictive nonlinear theories for multiscale modeling of heterogeneous materials

Concurrent multiscale modeling of three dimensional crack and dislocation propagation

Automatic image-based stress analysis by the scaled boundary finite element method

We propose a method to couple a three-dimensional continuum domain to a molecular dynamics (MD) domain to simulate propagating cracks in dynamics. The continuum domain is treated by an extended finite element method, to handle the discontinuities. The coupling is based on the Bridging Domain Method (BDM) which blends the continuum and atomistic energies. The Lennard-Jones potential is used to model the interactions in the atomistic domain and the Cauchy-Born rule is used to compute the material behaviour in the continuum domain. To our knowledge, it is the first time that a three dimensional extended bridging domain method is reported. To show the suitability of the proposed method, a three-dimensional crack problem with an atomistic region around the crack front is solved. The results show that the method is capable of handling crack propagation and dislocation nucleation.

/pdf/molecular-dynamics-xfem-coupling-by-a-three-dimensional-53yac8t4ih.pdf

Hossein Talebi

Papers

A computational library for multiscale modeling of material failure

Concurrent multiscale modeling of three dimensional crack and dislocation propagation

Automatic image-based stress analysis by the scaled boundary finite element method

Molecular dynamics/xfem coupling by a three-dimensional extended bridging domain with applications to dynamic brittle fracture

A semi-concurrent multiscale approach for modeling damage in nanocomposites