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Volumn 20, Issue 3, 2007, Pages 176-192

Smoothed molecular dynamics for large step time integration

Author keywords

Background grid; Critical time step; Material point method; Molecular dynamics

Indexed keywords

COMPUTER SIMULATION; INTEGRATION; SINGLE CRYSTALS;

EID: 34547760310     PISSN: 15261492     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (18)

References (40)
  • 1
    • 0036683069 scopus 로고    scopus 로고
    • Predicting trends in rate parameters for self-diffusion on fee metal surfaces
    • Agrawal, P. M.; Rice, B. M.; Thompson, D. L. (2002): Predicting trends in rate parameters for self-diffusion on fee metal surfaces. Surf. Sci., vol. 515, pp. 21-35.
    • (2002) Surf. Sci , vol.515 , pp. 21-35
    • Agrawal, P.M.1    Rice, B.M.2    Thompson, D.L.3
  • 3
    • 48749148224 scopus 로고
    • Rattle: A 'velocity' version of the shake algorithm for molecular dynamics calculations
    • Andersen, H. C. (1983): Rattle: A 'velocity' version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys., vol. 52, pp.24-34.
    • (1983) J. Comput. Phys , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 4
    • 0008581750 scopus 로고    scopus 로고
    • On some difficulties in integrating highly oscillatory hamiltonian systems
    • Ascher, U.; Reich, S. (1998): On some difficulties in integrating highly oscillatory hamiltonian systems. Lecture Notes in Computational Science and Engineering, vol. 4, pp. 281-296.
    • (1998) Lecture Notes in Computational Science and Engineering , vol.4 , pp. 281-296
    • Ascher, U.1    Reich, S.2
  • 5
    • 0033293798 scopus 로고    scopus 로고
    • The midpoint scheme and variants for hamiltonian systems: Advantages and pitfalls
    • Ascher, U.; Reich, S. (2000): The midpoint scheme and variants for hamiltonian systems: Advantages and pitfalls. SIAM Journal on Scientific Computing, vol. 21, pp. 1045-1065.
    • (2000) SIAM Journal on Scientific Computing , vol.21 , pp. 1045-1065
    • Ascher, U.1    Reich, S.2
  • 7
    • 0027666891 scopus 로고
    • Explicit multi-time step integration for first and second order finite element semidiscretizations
    • Belytschko, T.; Lu, Y. Y. (1993): Explicit multi-time step integration for first and second order finite element semidiscretizations. Comput. Meth. Appl. Mech. Eng., vol. 108, pp. 353-383.
    • (1993) Comput. Meth. Appl. Mech. Eng , vol.108 , pp. 353-383
    • Belytschko, T.1    Lu, Y.Y.2
  • 8
    • 17244374413 scopus 로고    scopus 로고
    • Concurrent coupling of length scales: Methodology and application
    • Broughton, J. Q.; Abraham, F. F.; Bernstein, N.; Kaxiras, E. (1999): Concurrent coupling of length scales: Methodology and application. Phys. Rev. B, vol. 60, pp. 2391-2403.
    • (1999) Phys. Rev. B , vol.60 , pp. 2391-2403
    • Broughton, J.Q.1    Abraham, F.F.2    Bernstein, N.3    Kaxiras, E.4
  • 9
    • 0002133110 scopus 로고    scopus 로고
    • Chun, H. M.; Padilla, C. E.; Chin, D. N.; M. W.; Karlov, V. I.; Alper, H. E.; Soosaar, K.; Blair, K. B.; Becker, O. M.; Caves, L. S. D.; Nagle, R.; Haney, D. N.; Farmer, B. L. (2000): Mbo(n)d: A multibody method for long-time molecular dynamics simulations. J. Comput. Chem., 21, pp. 159-184.
    • Chun, H. M.; Padilla, C. E.; Chin, D. N.; M. W.; Karlov, V. I.; Alper, H. E.; Soosaar, K.; Blair, K. B.; Becker, O. M.; Caves, L. S. D.; Nagle, R.; Haney, D. N.; Farmer, B. L. (2000): Mbo(n)d: A multibody method for long-time molecular dynamics simulations. J. Comput. Chem., vol. 21, pp. 159-184.
  • 10
    • 0142087541 scopus 로고    scopus 로고
    • Optimal reduced dimensional representation of classical molecular dynamics
    • Dey, B. K.; Rabitz, H.; Askar, A. (2003): Optimal reduced dimensional representation of classical molecular dynamics. J. Chem. Phys., vol. 119, pp. 5379-5388.
    • (2003) J. Chem. Phys , vol.119 , pp. 5379-5388
    • Dey, B.K.1    Rabitz, H.2    Askar, A.3
  • 11
    • 0000530285 scopus 로고
    • Time-reversible multiple time scale ab initio molecular dynamics
    • Gibson, D. A.; Carter, E. A. (1993): Time-reversible multiple time scale ab initio molecular dynamics. J. Phys. Chem., vol. 97, pp. 13429-13434.
    • (1993) J. Phys. Chem , vol.97 , pp. 13429-13434
    • Gibson, D.A.1    Carter, E.A.2
  • 12
    • 84963146276 scopus 로고
    • Generalized verlet algorithm for efficient molecular dynamics simulations with longrange interactions
    • Grubmuller, H.; Heller, H.; Windemuth, A.; et al (1991): Generalized verlet algorithm for efficient molecular dynamics simulations with longrange interactions. Molecular Simulations, vol. 6, pp. 121-142.
    • (1991) Molecular Simulations , vol.6 , pp. 121-142
    • Grubmuller, H.1    Heller, H.2    Windemuth, A.3
  • 14
    • 0000504254 scopus 로고
    • A multiple-time-step molecular dynamics algorithm for macromolecules
    • Humphreys, D. D.; Friesner, R. A.; Berne, B. J. (1994): A multiple-time-step molecular dynamics algorithm for macromolecules. J. Phys. Chem., vol. 98, pp. 6885-6892.
    • (1994) J. Phys. Chem , vol.98 , pp. 6885-6892
    • Humphreys, D.D.1    Friesner, R.A.2    Berne, B.J.3
  • 17
    • 0000921742 scopus 로고    scopus 로고
    • Longer time steps for molecular dynamics
    • Izaguirre, J. A.; Reich, S.; Skeel, R. D. (1999): Longer time steps for molecular dynamics. J. Chem. Phys., vol. 110, pp. 9853-9864.
    • (1999) J. Chem. Phys , vol.110 , pp. 9853-9864
    • Izaguirre, J.A.1    Reich, S.2    Skeel, R.D.3
  • 18
    • 16444380912 scopus 로고
    • Analytical nearest-neighbor model for fee metals
    • Johnson, R. A. (1988): Analytical nearest-neighbor model for fee metals. Phys. Rev. B, vol. 37, pp. 3924-3931.
    • (1988) Phys. Rev. B , vol.37 , pp. 3924-3931
    • Johnson, R.A.1
  • 19
    • 84968499113 scopus 로고
    • Symplectic integration of constrained hamiltonian systems
    • Leimkuhler, B.; Reich, S. (1994): Symplectic integration of constrained hamiltonian systems. Math. Comp., vol. 63, pp. 589-605.
    • (1994) Math. Comp , vol.63 , pp. 589-605
    • Leimkuhler, B.1    Reich, S.2
  • 20
    • 26844438929 scopus 로고    scopus 로고
    • Multiple time step molecular dynamics simulation for interaction between dislocations and grain boundaries
    • Li, X.; Yang, W. (2005): Multiple time step molecular dynamics simulation for interaction between dislocations and grain boundaries. Acta Mechanica Sinica, vol. 21, pp. 371-379.
    • (2005) Acta Mechanica Sinica , vol.21 , pp. 371-379
    • Li, X.1    Yang, W.2
  • 21
    • 33745559708 scopus 로고    scopus 로고
    • Multiscale simulation from atomisitic to continuum - coupling molecular dynamics (md) with the material point method (mpm)
    • Lu, H.; Daphalapurkar, N. P.; Wang, B.; Roy, S.; Komanduri, R. (2006): Multiscale simulation from atomisitic to continuum - coupling molecular dynamics (md) with the material point method (mpm). Philos. Mag., vol. 86, pp. 2971-2994.
    • (2006) Philos. Mag , vol.86 , pp. 2971-2994
    • Lu, H.1    Daphalapurkar, N.P.2    Wang, B.3    Roy, S.4    Komanduri, R.5
  • 22
    • 0035914597 scopus 로고    scopus 로고
    • An abnormal strain rate effect on tensile behavior in nanocrystalline copper
    • Lu, L.; Li, S. X.; Lu, K. (2001): An abnormal strain rate effect on tensile behavior in nanocrystalline copper. Scripta Materialia, vol. 45, pp. 1163-1169.
    • (2001) Scripta Materialia , vol.45 , pp. 1163-1169
    • Lu, L.1    Li, S.X.2    Lu, K.3
  • 23
    • 0346946971 scopus 로고    scopus 로고
    • Verlet-i/r-respa/impulse is limited by nonlinear instabilities
    • Ma, Q.; Izaguirre, J. A.; Skeel, R. D. (2003): Verlet-i/r-respa/impulse is limited by nonlinear instabilities. SIAM J. Sci. Comput., vol. 24, pp. 1951-1973.
    • (2003) SIAM J. Sci. Comput , vol.24 , pp. 1951-1973
    • Ma, Q.1    Izaguirre, J.A.2    Skeel, R.D.3
  • 24
    • 0001787214 scopus 로고
    • Smoothed dynamics of highly oscillatory hamiltonian systems
    • Reich, S. (1995): Smoothed dynamics of highly oscillatory hamiltonian systems. Physica D, vol. 89, pp.28-42.
    • (1995) Physica D , vol.89 , pp. 28-42
    • Reich, S.1
  • 25
    • 0043084528 scopus 로고    scopus 로고
    • Enhanced energy conserving method
    • Reich, S. (1996): Enhanced energy conserving method. BIT, vol. 36, pp. 122-134.
    • (1996) BIT , vol.36 , pp. 122-134
    • Reich, S.1
  • 26
    • 0007026709 scopus 로고    scopus 로고
    • Multiple time scales in classical and quantum-classical molecular dynamics
    • Reich, S. (1999): Multiple time scales in classical and quantum-classical molecular dynamics. J. Comput. Phys., vol. 151, pp. 49-73.
    • (1999) J. Comput. Phys , vol.151 , pp. 49-73
    • Reich, S.1
  • 27
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C (1977): Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput. Phys., vol. 23, pp. 327-341.
    • (1977) J Comput. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 28
    • 0001310692 scopus 로고    scopus 로고
    • Nonlinear resonance artifacts in molecular dynamics simulations
    • Schlick, T.; Mandziuk, M.; Skeel, R. D.; Srinivas, K. (1998): Nonlinear resonance artifacts in molecular dynamics simulations. J. Comput. Phys., vol 140, pp. 1-29.
    • (1998) J. Comput. Phys , vol.140 , pp. 1-29
    • Schlick, T.1    Mandziuk, M.2    Skeel, R.D.3    Srinivas, K.4
  • 29
    • 85190251461 scopus 로고    scopus 로고
    • Schlick, T.; Skeel, R. D.; Brunger, A. T.; Kale, L. V.; Board Jr., J. A.; Hermans, J.; Schulten, K. (1999): Algorithmic challenges in computational molecular biophysics. J. Comput. Phys., 151, pp. 9-48.
    • Schlick, T.; Skeel, R. D.; Brunger, A. T.; Kale, L. V.; Board Jr., J. A.; Hermans, J.; Schulten, K. (1999): Algorithmic challenges in computational molecular biophysics. J. Comput. Phys., vol. 151, pp. 9-48.
  • 30
    • 3242741931 scopus 로고    scopus 로고
    • Multiscale simulation based on the meshless local petrov-galerkin (mlpg) method
    • Shen, S.; Atluri, S. N. (2004): Multiscale simulation based on the meshless local petrov-galerkin (mlpg) method. CMES: Computer Modeling in Engineering & Sciences, vol. 5, pp. 235-255.
    • (2004) CMES: Computer Modeling in Engineering & Sciences , vol.5 , pp. 235-255
    • Shen, S.1    Atluri, S.N.2
  • 31
    • 13244288044 scopus 로고    scopus 로고
    • A tangent stiffness mlpg method for atom/continuum multiscale simualtion
    • Shen, S.; Atluri, S. N. (2005): A tangent stiffness mlpg method for atom/continuum multiscale simualtion. CMES: Computer Modeling in Engineering & Sciences, vol. 7, pp. 49-67.
    • (2005) CMES: Computer Modeling in Engineering & Sciences , vol.7 , pp. 49-67
    • Shen, S.1    Atluri, S.N.2
  • 32
  • 33
    • 0028493382 scopus 로고
    • Atomistic/continuum simulation of interfacial fracture, part ii: Atomistic /dislocation/continuum simulation
    • Tan, H. L.; Yang, W. (1994): Atomistic/continuum simulation of interfacial fracture, part ii: Atomistic /dislocation/continuum simulation. Acta Mechanica Sinica, vol. 10, pp. 237-249.
    • (1994) Acta Mechanica Sinica , vol.10 , pp. 237-249
    • Tan, H.L.1    Yang, W.2
  • 34
    • 33646650705 scopus 로고
    • Reversible multiple time scale molecular dynamics
    • Tuckerman, M.; Berne, B. J.; Martyna, G. J. (1992): Reversible multiple time scale molecular dynamics. J. Chem. Phys., vol. 97, pp. 1990-2201.
    • (1992) J. Chem. Phys , vol.97 , pp. 1990-2201
    • Tuckerman, M.1    Berne, B.J.2    Martyna, G.J.3
  • 35
    • 22944467757 scopus 로고
    • Computer 'experiments' on classical fluids, i. thermodynamical properties of lennard-jones molecules
    • Verlet, L. (1967): Computer 'experiments' on classical fluids, i. thermodynamical properties of lennard-jones molecules. Phys. Rev., vol. 159, pp. 98-103.
    • (1967) Phys. Rev , vol.159 , pp. 98-103
    • Verlet, L.1
  • 36
    • 0042858270 scopus 로고    scopus 로고
    • Coupling of atomistic and continuum simulation using a bridging scale decomposition
    • Wagner, G. J.; Liu, W. K. (2003): Coupling of atomistic and continuum simulation using a bridging scale decomposition. J. Comput. Phys., vol. 190, pp. 249-274.
    • (2003) J. Comput. Phys , vol.190 , pp. 249-274
    • Wagner, G.J.1    Liu, W.K.2
  • 37
    • 84913583406 scopus 로고
    • Lin: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal model techniques
    • Zhang, G.; Schlick, T. (1993): Lin: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal model techniques. J. Comput. Chem., vol. 14, pp. 1212-1233.
    • (1993) J. Comput. Chem , vol.14 , pp. 1212-1233
    • Zhang, G.1    Schlick, T.2
  • 38
    • 0001299323 scopus 로고
    • The langevin/implicit-euler/normal- mode scheme for molecular dynamics at large time steps
    • Zhang, G.; Schlick, T. (1994): The langevin/implicit-euler/normal- mode scheme for molecular dynamics at large time steps. J. Chem. Phys., vol. 101, pp. 4995-5013.
    • (1994) J. Chem. Phys , vol.101 , pp. 4995-5013
    • Zhang, G.1    Schlick, T.2
  • 39
    • 33646047713 scopus 로고    scopus 로고
    • An explicit material point finite element method for hyper velocity impact
    • Zhang, X.; Sze, K. Y.; Ma, S. (2006): An explicit material point finite element method for hyper velocity impact. Int. J. Numer. Meth. Engrg., vol. 66, pp. 689-706.
    • (2006) Int. J. Numer. Meth. Engrg , vol.66 , pp. 689-706
    • Zhang, X.1    Sze, K.Y.2    Ma, S.3
  • 40
    • 0035424713 scopus 로고    scopus 로고
    • Efficient multiple time step method for use with ewald and particle mesh ewald for large biomolecular systems
    • Zhou, R.; Harder, E.; Xu, H.; Berne, B. J. (2001): Efficient multiple time step method for use with ewald and particle mesh ewald for large biomolecular systems. J. Chem. Phys., vol. 115, pp. 2348-2358.
    • (2001) J. Chem. Phys , vol.115 , pp. 2348-2358
    • Zhou, R.1    Harder, E.2    Xu, H.3    Berne, B.J.4


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