Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques
Tài liệu tham khảo
Halgren, 2001, Polarizable force fields, Current Opinion Struct. Biol., 11, 236, 10.1016/S0959-440X(00)00196-2
Davis, 2008, Revised charge equilibration potential for liquid alkanes, J. Phys. Chem. B, 112, 8298, 10.1021/jp8003129
Brenner, 1990, Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films, Phys. Rev. B, 42, 9458, 10.1103/PhysRevB.42.9458
Brenner, 2002, A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons, J. Phys. Condens. Matter., 14, 783, 10.1088/0953-8984/14/4/312
Stuart, 2000, A reactive potential for hydrocarbons with intermolecular interactions, J. Chem. Phys., 112, 6472, 10.1063/1.481208
van Duin, 2001, ReaxFF: A reactive force field for hydrocarbons, J. Phys. Chem. A, 105, 9396, 10.1021/jp004368u
Nielson, 2005, Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes, J. Phys. Chem. A, 109, 493, 10.1021/jp046244d
Chenoweth, 2005, Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field, J. Am. Chem. Soc., 127, 7192, 10.1021/ja050980t
Buehler, 2007, Hierarchical chemo-nanomechanics of proteins: Entropic elasticity, protein unfolding and molecular fracture, J. Mech. Material Struct., 2, 1019, 10.2140/jomms.2007.2.1019
A. Thompson, H. Cho. (2010, Apr.) LAMMPS/ReaxFF potential. [Online]. Available: <http://lammps.sandia.gov/doc/pair_reax.html>.
Barrett, 1994
Plimpton, 1995, Fast parallel algorithms for short-range molecular dynamics, J. Comput. Phys., 117, 1, 10.1006/jcph.1995.1039
Nakano, 2008, De novo ultrascale atomistic simulations on high-end, Int. J. High Perf. Comput. Apps., 22, 113, 10.1177/1094342007085015
H.M. Aktulga, S. Pandit, A.C.T. van Duin, A. Grama, Reactive molecular dynamics: numerical methods and algorithmic techniques, SIAM J. Sci. Comput. (2011).
Park, 2009, Strain relaxation in Si/Ge/Si nanoscale bars from MD simulations, J. Appl. Phys., 106, 034304, 10.1063/1.3168424
Fogarty, 2010, A reactive simulation of the silica-water interface, J. Chem. Phys., 132, 174704, 10.1063/1.3407433
Rappe, 1991, Charge equilibration for molecular dynamics simulations, J. Phys. Chem., 95, 3358, 10.1021/j100161a070
Nakano, 1997, Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics, Comput. Phys. Commun., 104, 59, 10.1016/S0010-4655(97)00041-6
J.R. Shewchuk, An introduction to the conjugate gradient method without the agonizing pain, School of Computer Science, Carnegie Mellon University, Tech Report, August, 1994.
Saad, 1986, GMRES: A generalized minimal residual method for solving nonsymmetric linear systems, SIAM J. Sci. Stat. Comput., 7, 856, 10.1137/0907058
Saad, 2003
Fitch, 2003, an application framework for molecular simulation on Blue Gene, J. Parallel Distributed Comput., 63, 759, 10.1016/S0743-7315(03)00084-4
Phillips, 2005, Scalable molecular dynamics with NAMD, J. Comput. Chem., 26, 1781, 10.1002/jcc.20289
Hess, 2008, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theor. Comput., 4, 435, 10.1021/ct700301q
K.J. Bowers, E. Chow, H. Xu, R.O. Dror, M.P. Eastwood, B.A. Gregersen, J.L. Klepeis, I. Kolossvry, M.A. Moraes, F.D. Sacerdoti, J.K. Salmon, Y. Shan, D.E. Shaw, Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters, SC06, Tampa, Florida, Nov 11–17, 2006.
D.E. Shaw, M.M. Deneroff, R.O. Dror, J.S. Kuskin, R.H. Larson, J.K. Salmon, C. Young, B. Batson, K.J. Bowers, J.C. Chao, M.P. Eastwood, J. Gagliardo, J.P. Grossman, C.R. Ho, D.J. Ierardi, I. Kolossvry, J.L. Klepeis, T. Layman, C. McLeavey, M.A. Moraes, R. Mueller, E.C. Priest, Y. Shan, J. Spengler, M. Theobald, B. Towles, S.C. Wang, Anton: A special-purpose machine for molecular dynamics simulation, in: ISCA’07, San Diego, California, Jun 9–13, 2007.
Bowers, 2007, Zonal methods for the parallel execution of range-limited N-body simulations, J. Comput. Phys., 221, 303, 10.1016/j.jcp.2006.06.014
Linux Clusters Overview, 2009.<https://computing.llnl.gov/tutorials/linux_clusters/#OpteronMemoryConsiderations>.
Manguoglu, 2009, PSPIKE: a parallel hybrid sparse linear system solver, Lec. Notes Comput. Sci., 5704, 797, 10.1007/978-3-642-03869-3_74