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How to identify dislocations in molecular dynamics simulations?

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Abstract

Dislocations are of great importance in revealing the underlying mechanisms of deformed solid crystals. With the development of computational facilities and technologies, the observations of dislocations at atomic level through numerical simulations are permitted. Molecular dynamics (MD) simulation suggests itself as a powerful tool for understanding and visualizing the creation of dislocations as well as the evolution of crystal defects. However, the numerical results from the large-scale MD simulations are not very illuminating by themselves and there exist various techniques for analyzing dislocations and the deformed crystal structures. Thus, it is a big challenge for the beginners in this community to choose a proper method to start their investigations. In this review, we summarized and discussed up to twelve existing structure characterization methods in MD simulations of deformed crystal solids. A comprehensive comparison was made between the advantages and disadvantages of these typical techniques. We also examined some of the recent advances in the dynamics of dislocations related to the hydraulic fracturing. It was found that the dislocation emission has a significant effect on the propagation and bifurcation of the crack tip in the hydraulic fracturing.

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References

  1. Volterra V. Sur l’équilibre des corps élastiques multiplement connexes. Ann Sci Ecole Norm, 1907, S24: 401–517

    MathSciNet  Google Scholar 

  2. Taylor G I. The mechanism of plastic deformation of crystals. Part I. Theoretical. Proc R Soc Lond A, 1934, 145: 362–387

    Article  ADS  MATH  Google Scholar 

  3. Orowan E. Zur kristallplastizität. III. Z Phys, 1934, 89: 634–659

    Article  ADS  Google Scholar 

  4. Polanyi M. Über eine art gitterstörung, die einen kristall plastisch machen könnte. Z Phys, 1934, 89: 660–664

    Article  ADS  Google Scholar 

  5. Lesar R. Simulations of dislocation structure and response. Annu Rev B-Condens Matter Phys, 2014, 5: 375–407

    Article  Google Scholar 

  6. Frenkel J. Zur theorie der elastizitätsgrenze und der festigkeit kristallinischer körper. Z Phys, 1926, 37: 572–609

    Article  ADS  MATH  Google Scholar 

  7. Fleck N A, Muller G M, Ashby M F, et al. Strain gradient plasticity: Theory and experiment. Acta Metall Mater, 1994, 42: 475–487

    Article  Google Scholar 

  8. Yang W, Lee W B. Mesoplasticity and Its Applications. Berlin: Springer, 1993

    Book  Google Scholar 

  9. Chai X Z, Zhang Y, Liu B, et al. Effect of the V/III ratio during buffer layer growth on the yellow and blue luminescence in undoped GaN epilayer. Sci China-Phys Mech Astron, 2013, 56: 1694–1698

    Article  ADS  Google Scholar 

  10. Zhao C W, Xing Y M. Quantitative analysis of nanoscale deformation fields of a crack-tip in single-crystal silicon. Sci China-Phys Mech Astron, 2012, 55: 1088–1092

    Article  ADS  Google Scholar 

  11. Ma Y T, Zhang Y, Lu G H, et al. Effect of helium implantation on mechanical properties of niobium doped tungsten. Sci China-Phys Mech Astron, 2013, 56: 1396–1400

    Article  ADS  Google Scholar 

  12. Stukowski A. Computational analysis methods in atomistic modeling of crystals. JOM, 2014, 66: 399–407

    Article  Google Scholar 

  13. Lu G H, Zhang L. Connecting microscopic structure and macroscopic mechanical properties of structural materials from first-principles. Sci China-Phys Mech Astron, 2012, 55: 2305–2315

    Article  ADS  Google Scholar 

  14. Yuan F P. Atomistic simulation study of tensile deformation in bulk nanocrystalline bcc iron. Sci China-Phys Mech Astron, 2012, 55: 1657–1663

    Article  ADS  Google Scholar 

  15. Wu X L, Jiang P, Chen L, et al. Extraordinary strain hardening by gradient structure. Proc Natl Acad Sci USA, 2014, 111: 7197–7201

    Article  ADS  Google Scholar 

  16. Wang B B, Wang F C, Zhao Y P. Understanding formation mechanism of ZnO diatomic chain and multi-shell structure using physical mechanics: Molecular dynamics and first-principle simulations. Sci China-Phys Mech Astron, 2012, 55: 1138–1146

    Article  ADS  Google Scholar 

  17. Zhang Y Y, Wang F C, Zhao Y P. Negative differential resistance behavior of silicon monatomic chain encapsulated in carbon nanotubes. Comp Mater Sci, 2012, 62: 87–92

    Article  Google Scholar 

  18. Zang J L, Zhao Y P. Silicon nanowire reinforced by single-walled carbon nanotube and its applications to anti-pulverization electrode in lithium ion battery. Compos Part B Eng, 2012, 43: 76–82

    Article  Google Scholar 

  19. Yang Z Y, Lu Z X, Zhao Y P. Shape effects on the yield stress and deformation of silicon nanowires: A molecular dynamics simulation. J Appl Phys, 2009, 106: 023537

    Article  ADS  Google Scholar 

  20. Yang Z Y, Lu Z X, Zhao Y P. Atomistic simulation on size-dependent yield strength and defects evolution of metal nanowires. Comp Mater Sci, 2009, 46: 142–150

    Article  Google Scholar 

  21. An M R, Song H Y. Atomic simulations of influence of twinning on crack propagation of Al. Sci China-Phys Mech Astron, 2013, 56: 1938–1944

    Article  ADS  Google Scholar 

  22. Wu W P, Guo Y F, Wang Y S. Evolution of misfit dislocation network and tensile properties in Ni-based superalloys: A molecular dynamics simulation. Sci China-Phys Mech Astron, 2012, 55: 419–427

    Article  ADS  Google Scholar 

  23. Lin E Q, Niu L S, Shi H J, et al. Molecular dynamics study on the nano-void growth and coalescence at grain boundary. Sci China-Phys Mech Astron, 2012, 55: 86–93

    Article  ADS  Google Scholar 

  24. Wolf D, Yamakov V, Phillpot S R, et al. Deformation of nanocrystalline materials by molecular-dynamics simulation: Relationship to experiments? Acta Mater, 2005, 53: 1–40

    Article  Google Scholar 

  25. De Wette F W, Allen R E, Hughes D S, et al. Crystallization with a Lennard-Jones potential: A computer experiment. Phys Lett A, 1969, 29: 548–549

    Article  ADS  Google Scholar 

  26. Tang Q H. Effect of size on mechanical behavior of Au pillars by molecular dynamics study. Sci China-Phys Mech Astron, 2012, 55: 1111–1117

    Article  ADS  Google Scholar 

  27. Tang Q H, Wang T C, Shang B S, et al. Thermodynamic properties and constitutive relations of crystals at finite temperature. Sci China-Phys Mech Astron, 2012, 55: 918–926

    Article  ADS  Google Scholar 

  28. Yang Z Y, Jiao F F, Lu Z X, et al. Coupling effects of stress and ion irradiation on the mechanical behaviors of copper nanowires. Sci China-Phys Mech Astron, 2013, 56: 498–505

    Article  ADS  Google Scholar 

  29. Kang J W, Seo J J, Byun K R, et al. Defects in ultrathin copper nanowires: Atomistic simulations. Phys Rev B, 2002, 66: 125405

    Article  ADS  Google Scholar 

  30. Xu G Q, Demkowicz M. Healing of nanocracks by disclinations. Phys Rev Lett, 2013, 111: 145501

    Article  ADS  Google Scholar 

  31. Zhao Y P. Physical Mechanics of Surfaces and Interfaces (in Chinese). Beijing: Science Press, 2012

    Google Scholar 

  32. Stukowski A. Structure identification methods for atomistic simulations of crystalline materials. Model Simul Mater Sci Eng, 2012, 20: 045021

    Article  ADS  Google Scholar 

  33. Shimizu F, Ogata S, Li J. Theory of shear banding in metallic glasses and molecular dynamics calculations. Mater Trans, 2007, 48: 2923–2927

    Article  Google Scholar 

  34. Hara S, Li J. Adaptive strain-boost hyperdynamics simulations of stress-driven atomic processes. Phys Rev B, 2010, 82: 184114

    Article  ADS  Google Scholar 

  35. Li J. Atomeye: An efficient atomistic configuration viewer. Model Simul Mater Sci Eng, 2003, 11: 173–177

    Article  ADS  MATH  Google Scholar 

  36. Steinhardt P J, Nelson D R, Ronchetti M. Bond-orientational order in liquids and glasses. Phys Rev B, 1983, 28: 784–805

    Article  ADS  Google Scholar 

  37. Wolde P R T, Ruiz-Montero M J, Frenkel D. Numerical calculation of the rate of crystal nucleation in a Lennard-Jones system at moderate undercooling. J Chem Phys, 1996, 104: 9932–9947

    Article  ADS  Google Scholar 

  38. Lechner W, Dellago C. Accurate determination of crystal structures based on averaged local bond order parameters. J Chem Phys, 2008, 129: 114707

    Article  ADS  Google Scholar 

  39. Ackland G J, Jones A P. Applications of local crystal structure measures in experiment and simulation. Phys Rev B, 2006, 73: 054104

    Article  ADS  Google Scholar 

  40. Kelchner C L, Plimpton S, Hamilton J. Dislocation nucleation and defect structure during surface indentation. Phys Rev B, 1998, 58: 11085–11088

    Article  ADS  Google Scholar 

  41. Plimpton S. Fast parallel algorithms for short-range molecular dynamics. J Comput Phys, 1995, 117: 1–19

    Article  ADS  MATH  Google Scholar 

  42. Wang F C, Wu H A. Pinning and depinning mechanism of the contact line during evaporation of nano-droplets sessile on textured surfaces. Soft Matter, 2013, 9: 5703–5709

    Article  ADS  Google Scholar 

  43. Honeycutt J D, Andersen H C. Molecular dynamics study of melting and freezing of small Lennard-Jones clusters. J Phys Chem, 1987, 91: 4950–4963

    Article  Google Scholar 

  44. Faken D, Jónsson H. Systematic analysis of local atomic structure combined with 3D computer graphics. Comp Mater Sci, 1994, 2: 279–286

    Article  Google Scholar 

  45. Tsuzuki H, Branicio P S, Rino J P. Structural characterization of deformed crystals by analysis of common atomic neighborhood. Comput Phys Commun, 2007, 177: 518–523

    Article  ADS  Google Scholar 

  46. Stukowski A. Visualization and analysis of atomistic simulation data with OVITO—the Open Visualization Tool. Model Simul Mater Sci Eng, 2010, 18: 015012

    Article  ADS  Google Scholar 

  47. Gerbode S J, Agarwal U, Ong D C, et al. Glassy dislocation dynamics in 2D colloidal dimer crystals. Phys Rev Lett, 2010, 105: 078301

    Article  ADS  Google Scholar 

  48. Stukowski A, Albe K. Extracting dislocations and non-dislocation crystal defects from atomistic simulation data. Model Simul Mater Sci Eng, 2010, 18: 085001

    Article  ADS  Google Scholar 

  49. Stukowski A, Bulatov V V, Arsenlis A. Automated identification and indexing of dislocations in crystal interfaces. Model Simul Mater Sci Eng, 2012, 20: 085007

    Article  ADS  Google Scholar 

  50. Li J, Van Vliet K J, Zhu T, et al. Atomistic mechanisms governing elastic limit and incipient plasticity in crystals. Nature, 2002, 418: 307–310

    Article  ADS  Google Scholar 

  51. Li X Y, Wei Y J, Lu L, et al. Dislocation nucleation governed softening and maximum strength in nano-twinned metals. Nature, 2010, 464: 877–880

    Article  ADS  Google Scholar 

  52. Zhu T, Li J, Samanta A, et al. Interfacial plasticity governs strain rate sensitivity and ductility in nanostructured metals. Proc Natl Acad Sci USA, 2007, 104: 3031–3036

    Article  ADS  Google Scholar 

  53. Zhao Y P. Nano and Mesoscopic Mechanics (in Chinese). Beijing: Science Press, 2014

    Google Scholar 

  54. Jin Z H, Gumbsch P, Albe K, et al. Interactions between non-screw lattice dislocations and coherent twin boundaries in face-centered cubic metals. Acta Mater, 2008, 56: 1126–1135

    Article  Google Scholar 

  55. Yang W. Mechatronic Reliability: Electric Failures, Mechanical-Electrical Coupling, Domain Switching, Mass-Flow Instabilities. Berlin: Springer, 2003

    Google Scholar 

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Correspondence to YaPu Zhao.

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Contributed by ZHAO YaPu (Associate Editor)

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Li, D., Wang, F., Yang, Z. et al. How to identify dislocations in molecular dynamics simulations?. Sci. China Phys. Mech. Astron. 57, 2177–2187 (2014). https://doi.org/10.1007/s11433-014-5617-8

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  • DOI: https://doi.org/10.1007/s11433-014-5617-8

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