Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

Abstract We report on simulation technique and benchmarks for molecular dynamics simulations of the relaxation processes in solids and liquids using the graphics processing units (GPUs). The implementation of a many-body potential such as the embedded atom method (EAM) on GPU is discussed. The benchmarks obtained by LAMMPS and HOOMD packages for simple Lennard-Jones liquids and metals using EAM potentials are presented for both Intel CPUs and Nvidia GPUs. As an example the crystallization rate of the supercooled Al melt is computed.

[1]  Murray S. Daw,et al.  The embedded-atom method: a review of theory and applications , 1993 .

[2]  Vijay S. Pande,et al.  Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..

[3]  Matthew J. Kramer,et al.  Analysis of semi-empirical interatomic potentials appropriate for simulation of crystalline and liquid Al and Cu , 2008 .

[4]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[5]  Klaus Schulten,et al.  GPU-accelerated molecular modeling coming of age. , 2010, Journal of molecular graphics & modelling.

[6]  Michael J. Mehl,et al.  Interatomic potentials for monoatomic metals from experimental data and ab initio calculations , 1999 .

[7]  T. Motooka,et al.  Molecular-dynamics simulations of nucleation and crystallization in supercooled liquid silicon: Temperature-gradient effects , 2004 .

[8]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[9]  V. Stegailov,et al.  Cavitation in liquid metals under negative pressures. Molecular dynamics modeling and simulation , 2008, Journal of physics. Condensed matter : an Institute of Physics journal.

[10]  I. V. Morozov,et al.  Standards for molecular dynamics modelling and simulation of relaxation , 2005 .

[11]  Vladimir V. Stegailov Homogeneous and heterogeneous mechanisms of superheated solid melting and decay , 2005, Comput. Phys. Commun..

[12]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[13]  V. Stegailov,et al.  Structural transformations in single-crystal iron during shock-wave compression and tension: Molecular dynamics simulation , 2007 .

[14]  V. Stegailov,et al.  Dynamic fracture kinetics, influence of temperature and microstructure in the atomistic model of aluminum , 2010 .

[15]  A. Arnold,et al.  Harvesting graphics power for MD simulations , 2007, 0709.3225.

[16]  V. Stegailov,et al.  Atomistic simulation of the premelting of iron and aluminum: Implications for high-pressure melting-curve measurements , 2009 .