Chapter 4 Accelerated Molecular Dynamics Methods: Introduction and Recent Developments

Annual Reports in Computational Chemistry

Volumn 5, Issue , 2009, Pages 79-98

  Perez, Danny ^a   Uberuaga, Blas P ^b   Shim, Yunsic ^c   Amar, Jacques G ^c   Voter, Arthur F ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF TOLEDO   (United States)

Author keywords

accelerated dynamics; bond boost hyperdynamics; Cu(100); hyperdynamics; infrequent events; molecular dynamics; parallel accelerated dynamics; parallel replica dynamics; temperature accelerated dynamics; transition state theory

Indexed keywords

EID: 69349084577     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(09)00504-0     Document Type: Review

References (39)

1. Eyring H. The activated complex in chemical reactions. J. Chem. Phys. 3 (1935) 107-115
2. Pechukas P. Transition-state theory. Ann. Rev. Phys. Chem. 32 (1981) 159-177
3. Truhlar D.G., Garrett B.C., and Klippenstein S.J. Current status of transition-state theory. J. Phys. Chem. 100 (1996) 12771-12800
4. Voter A.F. Introduction to the kinetic Monte Carlo method. In: Sickafus K.E., Kotomin E.A., and Uberuaga B.P. (Eds). Radiation Effects in Solids (2006), Springer, NATO Publishing Unit, Dordrecht, The Netherlands 1-24
5. Voter A.F. Parallel replica method for dynamics of infrequent events. Phys. Rev. B 57 (1998) 13985-13988
6. Voter A.F., Montalenti F., and Germann T.C. Extending the time scale in atomistic simulation of materials. Ann. Rev. Mater. Res. 32 (2002) 321-346
7. Uberuaga B.P., Stuart S.J., and Voter A.F. Parallel replica dynamics for driven systems: derivation and application to strained nanotubes. Phys. Rev. B 75 (2007) 014301-1-9
8. 60. Phys. Rev. Lett. 91 10 (2003) 105901-105904
9. Kum O., Dickson B.M., Stuart S.J., Uberuaga B.P., and Voter A.F. Parallel replica dynamics with a heterogeneous distribution of barriers: application to n-hexadecane pyrolysis. J. Chem. Phys. 121 20 (2004) 9808-9819
10. Uberuaga B.P., Valone S.M., Baskes M.I., and Voter A.F. Accelerated molecular dynamics study of vacancies in Pu. AIP Conf. Proc. 673 (2003) 213-215
11. Uberuaga B.P., Hoagland R.G., Voter A.F., and Valone S.M. Direct transformation of vacancy voids to stacking fault tetrahedra. Phys. Rev. Lett. 99 (2007) 135501-1-4
12. Mishin Y., Suzuki A., Uberuaga B.P., and Voter A.F. Stick-slip behavior of grain boundaries studied by accelerated molecular dynamics. Phys. Rev. B 75 (2007) 224101-1-7
13. Duan Y., Halley J.W., Curtiss L., and Redfern P. Mechanisms of lithium transport in amorphous polyethylene oxide. J. Chem. Phys. 122 (2005) 054702-1-8
14. Warner D.H., Curtin W.A., and Qu S. Rate dependence of crack-tip processes predicts twinning trends in f.c.c. metals. Nat. Mater. 6 (2007) 876-881
15. Shirts M., and Pande V.S. Screen savers of the world unite!. Science 290 5498 (2000) 1903-1904
16. Voter A.F. A method for accelerating the molecular dynamics simulation of infrequent events. J. Chem. Phys. 106 (1997) 4665-4677
17. In: Berne B.J., Ciccotti G., and Coker D.F. (Eds). Classical and Quantum Dynamics in Condensed Phase Simulations (1998), World Scientific, River Edge, NJ
18. Valleau, J.P., Whittington, S.G. A guide to Monte Carlo for statistical mechanics: 1. Highways. In Statistical Mechanics. A. Modern Theoretical Chemistry (ed. B.J. Berne), Vol. 5, Plenum, New York, 1977, pp. 137-68.
19. Becker K.E., Mignogna M.H., and Fichthorn K.A. Accelerated molecular dynamics of temperature-programmed desorption. Phys. Rev. Lett. 102 (2009) 046101-1-4
20. Voter A.F. Hyperdynamics: accelerated molecular dynamics of infrequent events. Phys. Rev. Lett. 78 (1997) 3908-3911
21. Miron R.A., and Fichthorn K.A. Heteroepitaxial growth of Co/Cu(001): an accelerated molecular dynamics simulation study. Phys. Rev. B 72 (2005) 035415-1-7
22. Hamelberg D., Mongan J., and McCammon J.A. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J. Chem. Phys. 120 (2004) 11919-11929
23. Sørensen M.R., and Voter A.F. Temperature-accelerated dynamics for simulation of infrequent events. J. Chem. Phys. 112 (2000) 9599-9606
24. Montalenti F., and Voter A.F. Exploiting past visits or minimum-barrier knowledge to gain further boost in the temperature-accelerated dynamics method. J. Chem. Phys. 116 12 (2002) 4819-4828
25. Uberuaga B.P., Smith R., Cleave A.R., Henkelman G., Grimes R.W., Voter A.F., and Sickafus K.E. Dynamical simulations of radiation damage and defect mobility in MgO. Phys. Rev. B 71 10 (2005) 104102-1
26. Uberuaga B.P., Smith R., Cleave A.R., Montalenti F., Henkelman G., Grimes R.W., Voter A.F., and Sickafus K.E. Structure and mobility of defects formed from collision cascades in MgO. Phys. Rev. Lett. 92 11 (2004) 115505-4
27. Montalenti F., Sørensen M.R., and Voter A.F. Closing the gap between experiment and theory: crystal growth by temperature accelerated dynamics. Phys. Rev. Lett. 87 (2001) 126101-1-4
28. Sprague J.A., Montalenti F., Uberuaga B.P., Kress J.D., and Voter A.F. Simulation of growth of Cu on Ag(001) at experimental deposition rates. Phys. Rev. B 66 20 (2002) 205415-1-10
29. Harris D.J., Lavrentiev M.Y., Harding J.H., Allan N.L., and Purton J.A. Novel exchange mechanisms in the surface diffusion of oxides. J. Phys. Condens. Matter 16 13 (2004) L187-L192
30. Cogoni M., Uberuaga B.P., Voter A.F., and Colombo L. Diffusion of small self-interstitial clusters in silicon: temperature-accelerated tight-binding molecular dynamics simulations. Phys. Rev. B 71 12 (2005) 121203-1-4
31. Meerbach E., Schütte, C. Sequential change point detection in molecular dynamics trajectories. J. Multivariate Anal. Submitted for publication.
32. Miron R.A., and Fichthorn K.A. Accelerated molecular dynamics with the bond-boost method. J. Chem. Phys. 119 12 (2003) 6210-6216
33. Perez, D., Voter, A.F. Accelerating atomistic simulations through self-learning bond-boost hyperdynamics. Submitted for publication.
34. Shim Y., Amar J.G., Uberuaga B.P., and Voter A.F. Reaching extended length scales and time scales in atomistic simulations via spatially parallel temperature-accelerated dynamics. Phys. Rev. B 76 (2007) 205439-1-11
35. Shim Y., and Amar J.G. Semirigorous synchronous sublattice algorithm for parallel kinetic Monte Carlo simulations of thin film growth. Phys. Rev. B 71 (2005) 1254321-1-14
36. Botez C.E., Miceli P.F., and Stephens P.W. Temperature-dependent vacancy formation during the growth of Cu on Cu(001). Phys. Rev. B 66 (2002) 195413-1-6
37. Shim Y., Borovikov V., Uberuaga B.P., Voter A.F., and Amar J.G. Vacancy formation and strain in low-temperature Cu/Cu(100) growth. Phys. Rev. Lett. 101 (2008) 116101-1-4
38. Uberuaga B.P., Montalenti F., Germann T.C., and Voter A.F. Accelerated molecular dynamics methods. In: Yip S. (Ed). Handbook of Materials Modeling, Part A: Methods (2005), Springer, Dordrecht, The Netherlands 629 Part A
39. Miron R.A., and Fichthorn K.A. Multiple-time scale accelerated molecular dynamics: addressing the small-barrier problem. Phys. Rev. Lett. 93 (2004) 128301-1-4