Algorithms of GPU-enabled reactive force field (ReaxFF) molecular dynamics.

Reactive force field (ReaxFF), a recent and novel bond order potential, allows for reactive molecular dynamics (ReaxFF MD) simulations for modeling larger and more complex molecular systems involving chemical reactions when compared with computation intensive quantum mechanical methods. However, ReaxFF MD can be approximately 10-50 times slower than classical MD due to its explicit modeling of bond forming and breaking, the dynamic charge equilibration at each time-step, and its one order smaller time-step than the classical MD, all of which pose significant computational challenges in simulation capability to reach spatio-temporal scales of nanometers and nanoseconds. The very recent advances of graphics processing unit (GPU) provide not only highly favorable performance for GPU enabled MD programs compared with CPU implementations but also an opportunity to manage with the computing power and memory demanding nature imposed on computer hardware by ReaxFF MD. In this paper, we present the algorithms of GMD-Reax, the first GPU enabled ReaxFF MD program with significantly improved performance surpassing CPU implementations on desktop workstations. The performance of GMD-Reax has been benchmarked on a PC equipped with a NVIDIA C2050 GPU for coal pyrolysis simulation systems with atoms ranging from 1378 to 27,283. GMD-Reax achieved speedups as high as 12 times faster than Duin et al.'s FORTRAN codes in Lammps on 8 CPU cores and 6 times faster than the Lammps' C codes based on PuReMD in terms of the simulation time per time-step averaged over 100 steps. GMD-Reax could be used as a new and efficient computational tool for exploiting very complex molecular reactions via ReaxFF MD simulation on desktop workstations.

[1]  Adri C. T. van Duin,et al.  A reactive force-field (ReaxFF) Monte Carlo study of surface enrichment and step structure on yttria-stabilized zirconia , 2010 .

[2]  A. V. van Duin,et al.  Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field. , 2005, Journal of the American Chemical Society.

[3]  Adri C. T. van Duin,et al.  A reactive force field (ReaxFF) for zinc oxide , 2008 .

[4]  Lois Ember.  Firms to develop global environmental initiative , 1990 .

[5]  Francisco Vázquez,et al.  Automatic tuning of the sparse matrix vector product on GPUs based on the ELLR-T approach , 2012, Parallel Comput..

[6]  Adri C. T. van Duin,et al.  Combustion of an Illinois No. 6 coal char simulated using an atomistic char representation and the ReaxFF reactive force field , 2012 .

[7]  Ananth Grama,et al.  Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques , 2012, Parallel Comput..

[8]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born , 2012, Journal of chemical theory and computation.

[9]  M. Orio,et al.  Density functional theory , 2009, Photosynthesis Research.

[10]  Adri C. T. van Duin,et al.  Molecular dynamic simulation of aluminum–water reactions using the ReaxFF reactive force field , 2011 .

[11]  Wilfried J. Mortier,et al.  Electronegativity-equalization method for the calculation of atomic charges in molecules , 1986 .

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

[13]  Aiichiro Nakano,et al.  Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics , 1997 .

[14]  Dmitry Bedrov,et al.  Reactions of singly-reduced ethylene carbonate in lithium battery electrolytes: a molecular dynamics simulation study using the ReaxFF. , 2012, The journal of physical chemistry. A.

[15]  A. V. Duin,et al.  A Divide-and-Conquer/Cellular-Decomposition Framework for Million-to-Billion Atom Simulations of Chemical Reactions , 2007 .

[16]  A. V. Duin,et al.  ReaxFF: A Reactive Force Field for Hydrocarbons , 2001 .

[17]  William A. Goddard,et al.  Development and application of a ReaxFF reactive force field for oxidative dehydrogenation on vanadium oxide catalysts (The Journal of Physical Chemistry A (2008) 112C) , 2008 .

[18]  Francisco Vázquez,et al.  A new approach for sparse matrix vector product on NVIDIA GPUs , 2011, Concurr. Comput. Pract. Exp..

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

[20]  Jonathan P. Mathews,et al.  The molecular representations of coal – A review , 2012 .

[21]  Rajiv K. Kalia,et al.  A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations , 2008, Comput. Phys. Commun..

[22]  W. Goddard,et al.  Charge equilibration for molecular dynamics simulations , 1991 .

[23]  R. Dreizler,et al.  Density-Functional Theory , 1990 .

[24]  Kavoos Mirabbaszadeh,et al.  Interaction between single-walled carbon nanotubes and polymers: A molecular dynamics simulation study with reactive force field , 2012 .

[25]  R. Friesner.  Ab initio quantum chemistry: methodology and applications. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Yang Li,et al.  Reactive Bond-Order Simulations Using Both Spatial and Temporal Approaches to Parallelism , 2004 .