Online citations, reference lists, and bibliographies.
← Back to Search

Structure Identification Methods For Atomistic Simulations Of Crystalline Materials

A. Stukowski
Published 2012 · Materials Science, Physics, Mathematics

Cite This
Download PDF
Analyze on Scholarcy
Share
We discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.
This paper references
10.1016/J.ACTAMAT.2011.02.011
Atomistic processes controlling flow stress scaling during compression of nanoscale face-centered-cubic crystals
F. Sansoz (2011)
10.1016/J.JNUCMAT.2003.08.008
Modeling of dislocation-grain boundary interactions in FCC metals
M. D. Koning (2003)
10.1016/J.ACTAMAT.2004.11.027
Characterization and visualization of the lattice misfit associated with dislocation cores
C. S. Hartley (2005)
10.1063/1.438311
Interaction potentials and their effect on crystal nucleation and symmetry
C. Hsu (1979)
10.1016/0927-0256(94)90109-0
Systematic analysis of local atomic structure combined with 3D computer graphics
D. Faken (1994)
10.1063/1.3215722
VORO++: a three-dimensional voronoi cell library in C++.
Chris H. Rycroft (2009)
10.1103/PHYSREVB.57.7556
Defect production in collision cascades in elemental semiconductors and fcc metals
K. Nordlund (1998)
10.1088/0965-0393/18/1/015012
Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool
A. Stukowski (2009)
10.1021/J100303A014
Molecular dynamics study of melting and freezing of small Lennard-Jones clusters
J. Honeycutt (1987)
10.1103/PHYSREVLETT.69.620
Theoretical prediction and direct observation of the 9R structure in Ag.
Ernst (1992)
10.1098/rspa.1970.0189
Random packings and the structure of simple liquids. I. The geometry of random close packing
J. Finney (1970)
10.1016/j.bbr.2011.03.031
Characterizing Complex Particle Morphologies Through Shape Matching: Descriptors, Applications, and Algorithms
Ignacio Méndez Méndez Balbuena (2012)
10.1088/0965-0393/11/2/305
AtomEye: an efficient atomistic configuration viewer
J. Li (2003)
10.2307/2687299
Spatial Tessellations: Concepts and Applications of Voronoi Diagrams
A. Okabe (1992)
10.1103/PHYSREVB.58.11085
Dislocation nucleation and defect structure during surface indentation
C. L. Kelchner (1998)
10.1103/PHYSREVB.28.784
Bond-orientational order in liquids and glasses
P. Steinhardt (1983)
10.1103/PHYSREVB.82.224103
Nanotwinned fcc metals: Strengthening versus softening mechanisms
A. Stukowski (2010)
10.1145/355744.355745
An Algorithm for Finding Best Matches in Logarithmic Expected Time
J. Friedman (1977)
10.1016/J.JSSC.2005.06.011
Crystal nets as graphs: Terminology and definitions
Olaf Delgado-Friedrichs (2005)
10.1088/0965-0393/18/2/025016
Dislocation detection algorithm for atomistic simulations
A. Stukowski (2010)
10.1088/0965-0393/15/3/010
Common neighbour analysis for binary atomic systems
N. Lümmen (2007)
10.1103/PhysRevB.78.153202
Kinetic activation-relaxation technique: An off-lattice self-learning kinetic Monte Carlo algorithm
F. El-Mellouhi (2008)
10.1145/361002.361007
Multidimensional binary search trees used for associative searching
J. Bentley (1975)
10.1103/PHYSREVB.73.054104
Applications of local crystal structure measures in experiment and simulation
Graeme Ackland (2006)
10.1063/1.2977970
Accurate determination of crystal structures based on averaged local bond order parameters.
W. Lechner (2008)
10.1103/PHYSREVB.77.054201
Crystallization mechanisms for supercooled liquid Xe at high pressure and temperature: Hybrid Monte Carlo molecular simulations
C. Desgranges (2008)
The Art of Computer Programming Vol
D. Knuth (1998)
10.1088/0965-0393/18/8/085001
Extracting dislocations and non-dislocation crystal defects from atomistic simulation data
A. Stukowski (2010)
10.1016/j.cpc.2007.05.018
Structural characterization of deformed crystals by analysis of common atomic neighborhood
H. Tsuzuki (2007)
10.1088/0965-0393/20/3/035012
On the elastic–plastic decomposition of crystal deformation at the atomic scale
A. Stukowski (2012)
10.3367/UFNe.0182.201207b.0701
The puzzle of the $ \gamma\to\alpha$ and other phase transitions in cerium
A. Nikolaev (2012)
10.1006/JCPH.1995.1039
Fast parallel algorithms for short-range molecular dynamics
S. Plimpton (1993)
10.1107/S0108767303012017
Identification of and symmetry computation for crystal nets.
Olaf Delgado-Friedrichs (2003)
10.1145/321921.321925
An Algorithm for Subgraph Isomorphism
J. Ullmann (1976)
Theory of crystal dislocations
F. R. N. Nabarro (1987)
10.1103/PhysRevB.85.184203
Scalable parallel Monte Carlo algorithm for atomistic simulations of precipitation in alloys
B. Sadigh (2012)



This paper is referenced by
10.1088/0965-0393/24/5/055019
Molecular dynamics simulations of the mechanisms controlling the propagation of bcc/fcc semi-coherent interfaces in iron
X. Ou (2016)
10.1063/1.4966397
Simulation of a nonequilibrium phase transition initiated by the volumetric heat source using a molecular dynamics method
S. Korostelev (2016)
10.1088/1361-651X/aaaf94
A unified framework for heat and mass transport at the atomic scale
M. Ponga (2018)
10.1016/J.MATLET.2017.02.005
Plastic deformation of Cu single crystals containing an elliptic cylindrical void
Shuozhi Xu (2017)
10.15407/MFINT.38.10.1303
A Study of Atomic Displacements Produced in Cascades in Irradiated $\alpha$-Zr by Using Molecular Dynamics Simulations
Y. M. Ovcharenko (2016)
10.1063/1.4935452
Influence of phase transition on shock-induced spallation in nanocrystalline iron
N. Gunkelmann (2015)
10.1016/J.JNONCRYSOL.2018.04.062
Effect of amorphous phase on the plastic deformation mechanism of Mg: A molecular dynamics study
H. Y. Song (2018)
10.1016/J.PHYSLETA.2017.01.027
Molecular dynamics simulations of tension–compression asymmetry in nanocrystalline copper
K. Zhou (2017)
10.1039/C7RA02611K
Sintering of multiple Cu–Ag core–shell nanoparticles and properties of nanoparticle-sintered structures
J. Wang (2017)
10.1007/s00894-020-04361-0
Atomistic investigation on effect of Ca doping ratio on mechanical behaviors of nanocrystalline Mg-Ca alloys
F. Gao (2020)
10.1016/j.ijplas.2019.10.009
Molecular dynamics simulations on nanocrystalline super-elastic NiTi shape memory alloy by addressing transformation ratchetting and its atomic mechanism
B. Wang (2020)
10.1134/s1029959919050084
Effect of the Nanorod Size on Energy Absorption at the Microlevel under Cyclic Loading
I. Golovnev (2019)
10.1016/J.ACTAMAT.2018.09.038
Grain boundary segregation and intermetallic precipitation in coarsening resistant nanocrystalline aluminum alloys
A. Devaraj (2019)
10.1134/S1061933X19020066
Molecular Dynamics Simulation of Unstable Equilibrium of a Spherical Nucleus for Determining the Interfacial Energy in a Pb–Cu Two-Component System
V. Korolev (2019)
10.1016/j.actamat.2019.10.006
Dynamic martensitic phase transformation in single-crystal silver microcubes
R. Thevamaran (2020)
10.1016/j.jcrysgro.2019.125266
System size effect on crystal nuclei morphology in supercooled metallic melt
E. Kirova (2019)
10.1016/J.SCRIPTAMAT.2018.05.011
Solute effects on interfacial dislocation emission in nanomaterials: nucleation site competition and neutralization
V. Borovikov (2017)
10.1016/J.IJPLAS.2017.12.005
Shock-induced plasticity of semi-coherent 111 Cu-Ni multilayers
Meizhen Xianga (2018)
10.1016/J.MSEA.2016.01.055
Molecular dynamics simulation of effects of twin interfaces on Cu/Ni multilayers
Tao Fu (2016)
10.1002/9783527699025.CH22
Molecular Dynamics Analysis of Nanostructures
Xiaowang Zhou (2016)
10.1557/JMR.2019.141
Size effects on thermomechanical failure of layered structure with generalized particle dynamics multiscale methods
Jinghong Fan (2019)
10.1007/s10853-017-1495-6
Indentation into an Al/Si composite: enhanced dislocation mobility at interface
Z. Zhang (2017)
10.1016/j.ijsolstr.2020.02.003
A stress analysis method for molecular dynamics systems
J. Yang (2020)
On Open and Strong-Scaling Tools for Atom Probe Crystallography: High-Throughput Methods for Indexing Crystal Structure and Orientation
Markus Kühbach (2020)
10.1088/1741-4326/ab6061
Atomistic simulations of helium, hydrogen, and self-interstitial diffusion inside dislocation cores in tungsten
N. Mathew (2020)
10.1016/J.ACTAMAT.2018.03.058
GeV ion irradiation of NiFe and NiCo: Insights from MD simulations and experiments
A. Leino (2018)
10.1016/J.ACTAMAT.2016.12.011
Atomistic simulations of dislocations in a model BCC multicomponent concentrated solid solution alloy
S. Rao (2016)
10.1088/2053-1591/ab5531
Atomic insights in crystallization of liquid Cu on single crystal Ta and amorphous Ta
Xianglai Gan (2019)
10.1016/J.COMMATSCI.2019.109158
Dislocation interactions during nanoindentation of nickel-graphene nanocomposites
Vardan Hoviki Vardanyan (2019)
10.1088/1361-651X/ab8baa
Emergence of directionally-anisotropic mobility in a faceted Ʃ11 ⟨110⟩ tilt grain boundary in Cu
Megan J. McCarthy (2020)
10.1016/J.JNONCRYSOL.2019.04.035
Transport properties and abnormal breakdown of the Stokes-Einstein relation in computer simulated Al72Ni16Co12 metallic melt
Y. Zhou (2019)
10.1038/srep19535
Ru/Al Multilayers Integrate Maximum Energy Density and Ductility for Reactive Materials
K. Woll (2016)
See more
Semantic Scholar Logo Some data provided by SemanticScholar