Toolkit-based framework for scalable High Performance Standalone Molecular Dynamics simulations

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Date
2019-04
Authors
Ocaya, Richard Opio
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University of the Free State
Abstract
Computational modelling and simulation in materials science uses mathematical abstractions of particle-particle forces to postulate, develop and understand materials that are organized as particle systems. Real particle systems occupy macroscopic scales and can be costly to simulate in terms of hardware and software tools and simulation time. Even the most basic simulation can generate large amounts of intermediate data that requires innovative further processing to decipher its underlying physics or to answer fundamental questions about its material properties. These questions are increasingly being asked due the present furious academic and industrial interest in nanosized crystalline lattices. Of particular pertinence are questions of whether or not the properties of the nanostructures are identical to those of their macrostructures. In the light of this the primary focus of this contribution is the development of a tool to simulate face-centered cubic (fcc) particle systems on a “standalone” hardware platform, and to apply it to a specified particle system. The studied particle systems are to range from nanostructures to macrostructures. This thesis is thematically divided into two main parts. In the first part, comprising the first five chapters, we conduct a detailed survey of the current in computation, followed by a definition of the kinds of systems to which the study is applicable, and then we provide a detailed but not overwhelming description of the tool development, with numerous actual codes and examples. This part culminates in a working tool, abbreviated VSV. In the second part, comprising the subsequent chapters, we apply the VSV and associated tools to solve actual physics problems in nanostructures thereby offering new approaches and results to answer the current questions. In developing VSV, we discuss the pairwise-particle potential and its integration into an embedded atom model (EAM) approach that is a cost-effective way to simulate fcc metallic lattice systems as a select case that has practical and industrial relevance. To do this, We chose the Sutton-Chen EAM as being suitable. This was followed by the application of VSV on a single computer as the “standalone” setting, and then on a small, four-computer cluster consisting of multi-core, multi-processors to test its scaling and parallelization. The test system consisted of 30,261 copper atoms in an arbitrary fcc lattice. The various simulations were then evaluated for performance enhancements in terms of execution speed and ease of application. The large amounts of intermediate data made it necessary to develop smaller extensions to the VSV tool to enable output visualization. These extensions were written in Visual Basic and Matlab. We then apply VSV to simulate the systems at low energies and suggest novel answers to various questions within the framework mentioned above. A first major, unwittingly observed result in the application of VSV is that it showed that bond lengths between any two particles appear to develop a temporal oscillation when perturbed by a nearby displaced atom. These oscillations are seen to propagate throughout the lattice and eventually form a standing wave pattern, through which temperature can be modelled. By applying perturbations in which the bond length oscillation amplitudes are constrained to small values by deliberately applied perturbations, we found that the use of an elastic, Hooke’s Law model results in a faithful reproduction of the known elastic constants for the copper material on which it was tested. Thus, we suggest and develop a unique impulse and oscillation method that is useful to calculate the elastic properties of fcc nanostructures. A second result is the extension of this impulse-oscillation method to postulate a way to initiate wave-like energy transfer through the lattice. These waves are shown to be phonons and by constraining the energy to the first Brillouin zone we show that the temperature behavior of the lattice can be estimated. A third result is that VSV enables the computation of the diffusion in a nanosized lattice. Furthermore, we apply standard diffusion models to a low temperature regime and calculate the diffusion constants of the lattice using standard models. An important result is the indication that diffusion in such a collection of atoms in not driven by Brownian motion, but by the interplay of pair-wise 12-6 forces. We also show that the lattice atoms can spontaneously coalesce into a shape that is guided by the global minimum of potential energy. Finally, VSV also shows how growth into bigger fcc structures can be simulated through atom captures. The foregoing results are compared with the literature values and the good agreements indicate that it as a reasonable new and cost effective way to investigate many of the properties of fcc lattices. Aspects of the research have been published in a book chapter, journals and presented at international conferences. Finally, we present the concluding remarks about research and suggest further directions in terms of further development of VSV and its applications to new and novel structures.
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Thesis (Ph.D. (Physics))--University of the Free State, 2019, Computational modelling, Simulation
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