Applications of local crystal structure measures in experiment and simulation

Ackland, Graeme J.; Jones, Andrew

doi:10.1103/physrevb.73.054104

Cited by 445 publications

(290 citation statements)

References 19 publications

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“…The bond angle analysis (BAA) is another powerful as well as robust method for analyzing the crystalline structures obtained from MD simulations, which has been published recently by Ackland and Jones [39]. The BAA method is based on the analysis of angular distribution function of different lattice types and crystal defects.…”

Section: Bond Angle Analysis (Baa)mentioning

confidence: 99%

How to identify dislocations in molecular dynamics simulations?

Wang

Yang

et al. 2014

Sci. China Phys. Mech. Astron.

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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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Section: Bond Angle Analysis (Baa)mentioning

confidence: 99%

How to identify dislocations in molecular dynamics simulations?

Wang

Yang

et al. 2014

Sci. China Phys. Mech. Astron.

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“…[51] and modified in Ref. [8] to improve the accuracy of identification of crystal structures in the presence of small lattice distortions.…”

Section: Structural Analysis Of Atomic Configurationsmentioning

confidence: 99%

Generation of subsurface voids and a nanocrystalline surface layer in femtosecond laser irradiation of a single-crystal Ag target

et al. 2015

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Structural transformations in a shallow surface region of a bulk Ag (001) target irradiated by a femtosecond laser pulse are investigated in large-scale atomistic simulations and experiments.The simulations reveal a complex interplay of fast laser melting, rapid resolidification, and the dynamic relaxation of laser-induced stresses that leads to the formation of a sub-surface porous region covered by a nanocrystalline surface layer. The generation of the porous region is consistent with the experimental observation of surface "swelling" occurring at laser fluences below the spallation/ablation threshold and may be related to the incubation effect in multi-pulse laser ablation of metals. The nanocrystalline layer is produced by massive nucleation of crystallites triggered by a deep undercooling of the melted surface region experiencing fast quenching at a rate on the order of 10 11 K/s. The predicted surface structure features random crystallographic orientation of nanograins and a high density of stacking faults, twins, and nanoscale twinned structural elements with five-fold symmetry, which suggests high hardness and possible enhancement of catalytic activity of the surface.

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“…The output file system.out can be used in place of system.in to restart the simulation. It is also in a format readable by BallViewer [26].…”

Section: Checkpoint/restartmentioning

confidence: 99%

The MOLDY short-range molecular dynamics package

Ackland

D'Mellow

Daraszewicz

et al. 2011

Computer Physics Communications

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We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by shortrange potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Moldy addresses the problem of many atoms (of order 10 6 ) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (ParrinelloRahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, morse or Lennard Jones. Thus the program is especially well suited to calculations of metals. KeywordsRestrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order-N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation ...

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Applications of local crystal structure measures in experiment and simulation

Cited by 445 publications

References 19 publications

How to identify dislocations in molecular dynamics simulations?

How to identify dislocations in molecular dynamics simulations?

Generation of subsurface voids and a nanocrystalline surface layer in femtosecond laser irradiation of a single-crystal Ag target

The MOLDY short-range molecular dynamics package

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