Visualization and Analysis Strategies for Atomistic Simulations

  • Alexander StukowskiEmail author
Part of the Springer Series in Materials Science book series (SSMATERIALS, volume 245)


An important aspect of many molecular dynamics studies is the meaningful visualization of computed atomic configurations and trajectories, often contributing a lot to the understanding of the investigated phenomena. This chapter introduces visualization programs and analysis tools that have been developed for working with the output of classical molecular dynamics and other atomistic simulation models. Basic analysis techniques relevant for nanomechanics problems are described, which help to reveal structural phases, defects, and local deformations in materials. Furthermore, this chapter gives an overview of the dislocation extraction algorithm, which is a computational method for the automated detection and identification of dislocation lines in atomistic crystal models.


Burger Vector Central Atom Dislocation Line Common Neighbor Length Scale Parameter 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    C. Begau, J. Hua, A. Hartmaier, A novel approach to study dislocation density tensors and lattice rotation patterns in atomistic simulations. J. Mech. Phys. Solids 60 (4), 711–722 (2012)CrossRefGoogle Scholar
  2. 2.
    V.V. Bulatov, W. Cai, Computer Simulations of Dislocations (Oxford University Press, Oxford, 2006)Google Scholar
  3. 3.
    H. Edelsbrunner, E.P. Mücke, Three-dimensional alpha shapes. ACM T. Graphic 13 (1), 43–72 (1994)CrossRefGoogle Scholar
  4. 4.
    M. Elsey, B. Wirth, Fast automated detection of crystal distortion and crystal defects in polycrystal images. Multiscale Model. Simul. 12, 1–24 (2014)CrossRefGoogle Scholar
  5. 5.
    J. Erlebacher, I. McCue, Geometric characterization of nanoporous metals. Acta Mater. 60, 6146–6174 (2012)CrossRefGoogle Scholar
  6. 6.
    D. Faken, H. Jonsson, Systematic analysis of local atomic structure combined with 3d computer graphics. Comput. Mater. Sci. 2 (2), 279–286 (1994)CrossRefGoogle Scholar
  7. 7.
    M.L. Falk, J.S. Langer, Dynamics of viscoplastic deformation in amorphous solids. Phys. Rev. E 57, 7192–7205 (1998)CrossRefGoogle Scholar
  8. 8.
    F.C. Frank, LXXXIII. Crystal dislocations – Elementary concepts and definitions. Philos. Mag. Ser. 7 42 (331), 809–819 (1951)Google Scholar
  9. 9.
    C.S. Hartley, Y. Mishin, Characterization and visualization of the lattice misfit associated with dislocation cores. Acta Mater. 53 (5), 1313–1321 (2005)CrossRefGoogle Scholar
  10. 10.
    J.D. Honeycutt, H.C. Andersen, Molecular dynamics study of melting and freezing of small Lennard-Jones clusters. J. Phys. Chem. 91 (19), 4950–4963 (1987)CrossRefGoogle Scholar
  11. 11.
    C.L. Kelchner, S.J. Plimpton, J.C. Hamilton, Dislocation nucleation and defect structure during surface indentation. Phys. Rev. B 58 (17), 11085 (1998)Google Scholar
  12. 12.
    A.S. Keys, C.R. Iacovella, S.C. Glotzer, Characterizing complex particle morphologies through shape matching: Descriptors, applications, and algorithms. J. Comp. Phys. 230 (17), 6438–6463 (2011)CrossRefGoogle Scholar
  13. 13.
    P.S. Landweber, E.A. Lazar, N. Patel, On fiber diameters of continuous maps. Am. Math. Mon. 123, 392–397 (2016). doi:  10.4169/amer.math.monthly.123.4.392 CrossRefGoogle Scholar
  14. 14.
    E.A. Lazar, J. Han, D.J. Srolovitz, Topological framework for local structure analysis in condensed matter. PNAS 112, E5769–E5776 (2015)CrossRefGoogle Scholar
  15. 15.
    B.-N.D. Ngô, A. Stukowski, N. Mameka, J. Markmann, K. Albe, J. Weissmüller, Anomalous compliance and early yielding of nanoporous gold. Acta Mater. 93, 144–155 (2015)CrossRefGoogle Scholar
  16. 16.
    J. Schäfer, A. Stukowski, K. Albe, Plastic deformation of nanocrystalline {Pd-Au} alloys: {On} the interplay of grain boundary solute segregation, fault energies and grain size. J. Appl. Phys. 114 (14), 143501 (2013)Google Scholar
  17. 17.
    F. Shimizu, S. Ogata, J. Li, Theory of shear banding in metallic glasses and molecular dynamics calculations. Mater. Trans. 48 (11), 2923–2927 (2007)CrossRefGoogle Scholar
  18. 18.
    A. Shrake, J.A. Rupley, Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79 (2), 351–371 (1973)CrossRefGoogle Scholar
  19. 19.
    A. Stukowski, Visualization and analysis of atomistic simulation data with OVITO–the open visualization tool. Model. Simul. Mater. Sci. Eng. 18 (1), 015012 (2010)Google Scholar
  20. 20.
    A. Stukowski, Structure identification methods for atomistic simulations of crystalline materials. Model. Simul. Mater. Sci. Eng. 20 (4), 045021 (2012)Google Scholar
  21. 21.
    A. Stukowski, Computational analysis methods in atomistic modeling of crystals. JOM 66 (3), 399–407 (2014)CrossRefGoogle Scholar
  22. 22.
    A. Stukowski, A triangulation-based method to identify dislocations in atomistic models. J. Mech. Phys. Solids 70, 314–319 (2014)CrossRefGoogle Scholar
  23. 23.
    A. Stukowski, K. Albe, Extracting dislocations and non-dislocation crystal defects from atomistic simulation data. Model. Simul. Mater. Sci. Eng. 18 (8), 085001 (2010)Google Scholar
  24. 24.
    A. Stukowski, K. Albe, D. Farkas, Nanotwinned fcc metals: Strengthening versus softening mechanisms. Phys. Rev. B 82 (22), 224103 (2010)Google Scholar
  25. 25.
    A. Stukowski, A. Arsenlis, On the elastic–plastic decomposition of crystal deformation at the atomic scale. Model. Simul. Mater. Sci. Eng. 20 (3), 035012 (2012)Google Scholar
  26. 26.
    A. Stukowski, V.V. Bulatov, A. Arsenlis, Automated identification and indexing of dislocations in crystal interfaces. Model. Simul. Mater. Sc. 20, 085007 (2012)CrossRefGoogle Scholar
  27. 27.
    E. Maras, O. Trushin, A. Stukowski, T. Ala-Nissila, H. Jónsson, Global transition path search for dislocation formation in Ge on Si(001). Comput. Phys. Commun. 205, 13–21 (2016)CrossRefGoogle Scholar
  28. 28.
    S. Wang, G. Lu, G. Zhang, A Frank scheme of determining the Burgers vectors of dislocations in a FCC crystal. Comput. Mater. Sci. 68, 396–401 (2013)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Technische Universität DarmstadtDarmstadtGermany

Personalised recommendations