EON: Software for long time simulations of atomic scale systems

Modelling and Simulation in Materials Science and Engineering

Volumn 22, Issue 5, 2014, Pages

  Chill, Samuel T ^a   Welborn, Matthew ^a   Terrell, Rye ^a   Zhang, Liang ^a   Berthet, Jean Claude ^b   Pedersen, Andreas ^b   Jónsson, Hannes ^b   Henkelman, Graeme ^a  

^a Section of Molecular Genetics and Microbiology   (United States)

^b UNIVERSITY OF ICELAND   (Iceland)

Author keywords

accelerated molecular dynamics; adaptive kinetic Monte Carlo; rare event dynamics; saddle points; transition state finding

Indexed keywords

COMPUTER ARCHITECTURE; DISTRIBUTED COMPUTER SYSTEMS; GLOBAL OPTIMIZATION; METAL NANOPARTICLES; MOLECULAR DYNAMICS; SIMULATED ANNEALING;

ACCELERATED MOLECULAR DYNAMICS; EVENT DYNAMICS; KINETIC MONTE CARLO; SADDLE POINT; TRANSITION STATE;

ATOMS;

EID: 84902465105     PISSN: 09650393     EISSN: 1361651X     Source Type: Journal    
DOI: 10.1088/0965-0393/22/5/055002     Document Type: Article

References (44)

1. Voter A F 1998 Parallel replica method for dynamics of infrequent events Phys. Rev. B 57 R13985-8
2. Voter A F 1997 Hyperdynamics: accelerated molecular dynamics of infrequent events Phys. Rev. Lett. 78 3908-11 (Pubitemid 127655393)
3. Miron R A and Fichthorn K A 2003 Accelerated molecular dynamics with the bond-boost method J. Chem. Phys. 119 6210-6
4. Henkelman G and Jónsson H 2001 Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table J. Chem. Phys. 115 9657-66 (Pubitemid 33147327)
5. Wales D J and Doye J P K 1997 Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms J. Phys. Chem. A 101 5111-6 (Pubitemid 127578169)
6. Goedecker S 2004 Minima hopping: an efficient search method for the global minimum of the potential energy surface of complex molecular systems J. Chem. Phys. 120 9911-7
7. Anderson D P 2004 Boinc: a system for public-resource computing and storage 5th IEEE/ACM Int. Workshop on Grid Computing (Pittsburgh, PA,) pp 4-10 (Pubitemid 40752119)
8. Cai X, Langtangen H P and Moe H 2005 On the performance of the python programming language for serial and parallel scientific computations Sci. Program. 13 31-56 (Pubitemid 40878670)
9. Jónsson H, Mills G and Jacobsen K W 1998 Nudged elastic band method for finding minimum energy paths of transitions Classical and Quantum Dynamics in Condensed Phase Simulations ed B J Berne et al (Singapore: World Scientific) pp 385-404
10. Bitzek E, Koskinen P, Fähler F, Moseler M and Gumbsch P 2006 Structural relaxation made simple Phys. Rev. Lett. 97 170201 (Pubitemid 44656233)
11. Hestenes M R and Steifel E 1952 Methods of conjugate gradients for solving linear systems J. Res. Natl Bur. Stand. 49 409-36
12. Nocedal J 1980 Updating quasi-Newton matrices with limited storage Math. Comput. 35 773-82
13. Plimpton S 1995 Fast parallel algorithms for short-range molecular dynamics J. Comput. Phys. 117 1-19
14. Kresse G and Hafner J 1993 Abinitio molecular dynamics for liquid metals Phys. Rev. B 47 R558-61
15. Mortensen J J, Hansen L B and Jacobsen K W 2005 Real-space grid implementation of the projector augmented wave method Phys. Rev. B 71 035109 (Pubitemid 40396389)
16. Daw M S and Baskes M I 1984 Embedded-atom method: derivation and application to impurities, surfaces, and other defects in metals Phys. Rev. B 29 6443-53
17. Voter A F and Chen S P 1987 Accurate interatomic potentials for Ni, Al and Ni3Al Mater. Res. Soc. Symp. Proc. 82 175-80
18. Jacobsen K, Stoltze P and Nørskov J K 1996 A semi-empirical effective medium theory for metals and alloys Surf. Sci. 366 394-402 (Pubitemid 126385604)
19. Lenosky T J, Sadigh B, Alonso E, Bulatov V V, Diaz de la Rubia T, Kim J, Voter A F and Kress J D 2000 Highly optimized empirical potential model of silicon Modelling Simul. Mater. Sci. Eng. 8 825 (Pubitemid 32073169)
20. Tersoff J 1988 Empirical interatomic potential for silicon with improved elastic properties Phys. Rev. B 38 9902
21. Justo J F, Bazant M Z, Kaxiras E, Bulatov V V and Yip S 1998 Interatomic potential for silicon defects and disordered phases Phys. Rev. B 58 2539
22. Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W and Klein M L 1983 Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 926-35
23. Vtsttools 2012 http://theory.cm.utexas.edu/vtsttools - ref-separator -
24. EON 2012 distributed computing project http://eon.ices.utexas.edu/ - ref-separator -
25. Nordugrid 2012 www.nordugrid.org/arc/ - ref-separator -
26. Zhang L, Chill S T and Henkelman G 2014 Distributed replica dynamics in preparation
27. Voter A F 2007 Introduction to the kinetic Monte Carlo method Radiation Effects in Solids (NATO Science Series II: Mathematics, Physics and Chemistry) ed K E Sickafus et al (Amsterdam: Springer) pp 1-23
28. Henkelman G and Jónsson H 1999 A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives J. Chem. Phys. 111 7010-22 (Pubitemid 129579526)
29. Horn R A and Johnson C R 1985 Matrix Analysis (Cambridge: Cambridge University Press)
30. Munro L J and Wales D J 1999 Defect migration in crystalline silicon Phys. Rev. B 59 3969
31. Malek R and Mousseau N 2000 Dynamics of Lennard-Jones clusters: a characterization of the activation-relaxation technique Phys. Rev. E 62 7723-8 (Pubitemid 32087991)
32. Xu L and Henkelman G 2008 Adaptive kinetic Monte Carlo for first-principles accelerated dynamics J. Chem. Phys. 129 114104
33. Novotny M A 1995 Monte carlo algorithms with absorbing Markov chains: fast local algorithms for slow dynamics Phys. Rev. Lett. 74 1-5
34. Grinstead C M and Snell J L 2003 Introduction to Probability 2nd edn (Providence, RI: American Mathematical Society)
35. Pedersen A, Berthet J C and Jónsson H 2012 Simulated annealing with coarse graining and distributed computing Lect. Notes Comput. Sci. 7134 34-44
36. Mendelev M I, Sordelet D J and Kramer M J 2007 Using atomistic computer simulations to analyze x-ray diffraction data from metallic glasses J. Appl. Phys. 102 043501 (Pubitemid 47353978)
37. Lawrence C P and Skinner J L 2003 Flexible TIP4P model for molecular dynamics simulation of liquid water Chem. Phys. Lett. 372 842-7 (Pubitemid 36535688)
38. Terrell R, Welborn M, Chill S T and Henkelman G 2012 Database of atomistic reaction mechanisms with application to kinetic Monte Carlo J. Chem. Phys. 137 015105
39. Wales D J and Scheraga H A 1999 Global optimization of clusters, crystals, and biomolecules Science 285 1368-72 (Pubitemid 29411661)
40. Allen M P and Tildesley D J 1987 Computer Simulation of Liquids (Oxford: Oxford Univ. Press)
41. White R P and Mayne H R 1998 An investigation of two approaches to basin hopping minimization for atomic and molecular clusters Chem. Phys. Lett. 289 463-8 (Pubitemid 128185997)
42. Iwamatsu M and Okabe Y 2004 Basin hopping with occasional jumping Chem. Phys. Lett. 399 396-400 (Pubitemid 40017545)
43. Sicher M, Mohr S and Goedecker S 2011 Efficient moves for global geometry optimization methods and their application to binary systems J. Chem. Phys. 134 044106
44. Jónsson H 2011 Simulation of surface processes Proc. Natl Acad. Sci. 108 944-9