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Volumn 38, Issue 4-5, 2012, Pages 245-259

Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques

Author keywords

Application of algorithms; High performance computing; Krylov subspace methods; Molecular dynamics; Numerical techniques; Parallel scaling and performance; Reactive force fields; Scientific computing

Indexed keywords

HIGH PERFORMANCE COMPUTING; KRYLOV SUBSPACE METHOD; NUMERICAL TECHNIQUES; PARALLEL SCALING AND PERFORMANCE; REACTIVE FORCE FIELD;

EID: 84858748702     PISSN: 01678191     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.parco.2011.08.005     Document Type: Article
Times cited : (831)

References (29)
  • 2
    • 48849103645 scopus 로고    scopus 로고
    • Revised charge equilibration potential for liquid alkanes
    • J.E. Davis, G.L. Warren, and S. Patel Revised charge equilibration potential for liquid alkanes J. Phys. Chem. B 112 2008 8298 8310
    • (2008) J. Phys. Chem. B , vol.112 , pp. 8298-8310
    • Davis, J.E.1    Warren, G.L.2    Patel, S.3
  • 3
    • 33644817086 scopus 로고
    • Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films
    • D.W. Brenner Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films Phys. Rev. B 42 1990 9458 9471
    • (1990) Phys. Rev. B , vol.42 , pp. 9458-9471
    • Brenner, D.W.1
  • 4
    • 0037017208 scopus 로고    scopus 로고
    • A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons
    • DOI 10.1088/0953-8984/14/4/312, PII S095389840231186X
    • D.W. Brenner, O.A. Shenderova, J.A. Harrison, S.J. Stuart, and S.B. Sinnott A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons J. Phys. Condens. Matter. 14 2002 783 802 (Pubitemid 34153770)
    • (2002) Journal of Physics Condensed Matter , vol.14 , Issue.4 , pp. 783-802
    • Brenner, D.W.1    Shenderova, O.A.2    Harrison, J.A.3    Stuart, S.J.4    Ni, B.5    Sinnott, S.B.6
  • 5
    • 0001256721 scopus 로고    scopus 로고
    • A reactive potential for hydrocarbons with intermolecular interactions
    • S.J. Stuart, A.B. Tutein, and J.A. Harrison A reactive potential for hydrocarbons with intermolecular interactions J. Chem. Phys. 112 2000 6472
    • (2000) J. Chem. Phys. , vol.112 , pp. 6472
    • Stuart, S.J.1    Tutein, A.B.2    Harrison, J.A.3
  • 7
    • 13444288029 scopus 로고    scopus 로고
    • 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
    • DOI 10.1021/jp046244d
    • K.D. Nielson, A.C.T. van Duin, J. Oxgaard, W-Q. Deng, and W.A. Goddard III 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 2005 493 499 (Pubitemid 40206807)
    • (2005) Journal of Physical Chemistry A , vol.109 , Issue.3 , pp. 493-499
    • Nielson, K.D.1    Van Duin, A.C.T.2    Oxgaard, J.3    Deng, W.-Q.4    Goddard III, W.A.5
  • 8
    • 18744389144 scopus 로고    scopus 로고
    • Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field
    • DOI 10.1021/ja050980t
    • K. Chenoweth, S. Cheung, A.C.T. van Duin, W.A. Goddard III, and E.M. Kober Simulations on the thermal decomposition of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field J. Am. Chem. Soc. 127 2005 7192 7202 (Pubitemid 40676744)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.19 , pp. 7192-7202
    • Chenoweth, K.1    Cheung, S.2    Van Duin, A.C.T.3    Goddard III, W.A.4    Kober, E.M.5
  • 9
    • 34548671447 scopus 로고    scopus 로고
    • Hierarchical chemo-nanomechanics of proteins: Entropic elasticity, protein unfolding and molecular fracture
    • M.J. Buehler Hierarchical chemo-nanomechanics of proteins: Entropic elasticity, protein unfolding and molecular fracture J. Mech. Material Struct. 2 6 2007 1019 1057
    • (2007) J. Mech. Material Struct. , vol.2 , Issue.6 , pp. 1019-1057
    • Buehler, M.J.1
  • 12
    • 0002467378 scopus 로고
    • Fast parallel algorithms for short-range molecular dynamics
    • S.J. Plimpton Fast parallel algorithms for short-range molecular dynamics J. Comput. Phys. 117 1995 1 19
    • (1995) J. Comput. Phys. , vol.117 , pp. 1-19
    • Plimpton, S.J.1
  • 15
    • 69149108328 scopus 로고    scopus 로고
    • Strain relaxation in Si/Ge/Si nanoscale bars from MD simulations
    • Y. Park, H.M. Aktulga, A.Y. Grama, and A. Strachan Strain relaxation in Si/Ge/Si nanoscale bars from MD simulations J. Appl. Phys. 106 2009 034304
    • (2009) J. Appl. Phys. , vol.106 , pp. 034304
    • Park, Y.1    Aktulga, H.M.2    Grama, A.Y.3    Strachan, A.4
  • 17
    • 33748481964 scopus 로고
    • Charge equilibration for molecular dynamics simulations
    • A.K. Rappe, and W.A. Goddard III Charge equilibration for molecular dynamics simulations J. Phys. Chem. 95 1991 3358 3363
    • (1991) J. Phys. Chem. , vol.95 , pp. 3358-3363
    • Rappe, A.K.1    Goddard Iii, W.A.2
  • 18
    • 0031212250 scopus 로고    scopus 로고
    • Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics
    • PII S0010465597000416
    • Aiichiro Nakano Parallel multilevel preconditioned conjugate-gradient approach to variable-charge molecular dynamics Comput. Phys. Commun. 104 1997 59 69 (Pubitemid 127400925)
    • (1997) Computer Physics Communications , vol.104 , Issue.1-3 , pp. 59-69
    • Nakano, A.1
  • 20
    • 0000048673 scopus 로고
    • GMRES: A generalized minimal residual method for solving nonsymmetric linear systems
    • Y. Saad, and M.H. Schultz GMRES: A generalized minimal residual method for solving nonsymmetric linear systems SIAM J. Sci. Stat. Comput. 7 1986 856 869
    • (1986) SIAM J. Sci. Stat. Comput. , vol.7 , pp. 856-869
    • Saad, Y.1    Schultz, M.H.2
  • 24
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theor. Comput. 4 3 2008 435 447
    • (2008) J. Chem. Theor. Comput. , vol.4 , Issue.3 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Van Der Spoel, D.3    Lindahl, E.4
  • 27
    • 33846148305 scopus 로고    scopus 로고
    • Zonal methods for the parallel execution of range-limited N-body simulations
    • K.J. Bowers, R.O. Dror, and D.E. Shaw Zonal methods for the parallel execution of range-limited N-body simulations J. Comput. Phys. 221 2007 303 329
    • (2007) J. Comput. Phys. , vol.221 , pp. 303-329
    • Bowers, K.J.1    Dror, R.O.2    Shaw, D.E.3
  • 29
    • 70350637491 scopus 로고    scopus 로고
    • PSPIKE: A parallel hybrid sparse linear system solver
    • M. Manguoglu, A. Sameh, and O. Schenk PSPIKE: a parallel hybrid sparse linear system solver Lec. Notes Comput. Sci. 5704 2009 797 808
    • (2009) Lec. Notes Comput. Sci. , vol.5704 , pp. 797-808
    • Manguoglu, M.1    Sameh, A.2    Schenk, O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.