Toolkit-based framework for scalable High Performance Standalone Molecular Dynamics simulations
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Date
2019-04
Authors
Ocaya, Richard Opio
Journal Title
Journal ISSN
Volume Title
Publisher
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.
Description
Keywords
Thesis (Ph.D. (Physics))--University of the Free State, 2019, Computational modelling, Simulation