Parallel Fast Multipole Method for Molecular Dynamics

We report on a parallel version of the Fast Multipole Method (FMM) implemented in the classical molecular dynamics code, NAMD (Not Another Molecular Dynamics program). This novel implementation of FMM aims to minimize interprocessor communication through the modification of the FMM grid to match the hybrid force and spatial decomposition scheme already present in NAMD. This new implementation has the benefit of replacing all-to-all communications broadcasts with direct communications between nearest neighbors. This results in a significant reduction in the amount of communication compared to earlier attempts to integrate FMM into common molecular dynamics programs. The early performance of FMM is similar to the existing electrostatics methods already in NAMD. In addition, tests of the stability and accuracy of the FMM algorithm in molecular dynamics as applied to several common solvated protein structures are discussed

Distribution independent parallel algorithms and software for hierarchical methods with applications to computational electromagnetics

Octrees are tree data structures used to represent multidimensional points in space. They are widely used in supporting hierarchical methods for scientific applications such as the N-body problem, molecular dynamics and smoothed particle hydrodynamics. The size of an octree is known to be dependent on the spatial distribution of points in the computational domain and is not just a function of the number of points. For this reason, run-time of an algorithm using octree that depends on the size of the octree is unknown for arbitrary distributions. In this thesis, we present the design and implementation of parallel algorithms for construction of compressed octrees and queries that are typically used by hierarchical methods. Our parallel algorithms and implementation strategies perform well irrespective of the spatial distribution of data, are communication efficient, and require no explicit load balancing. We also developed a software library which provides the functionality of parallel tree construction and various queries on compressed octrees. The purpose of the library is to enable rapid development of applications and to allow application developers to use efficient parallel algorithms without necessity of having detailed knowledge of the algorithms or of implementing them. To demonstrate the performance of our algorithms and to show the effectiveness of the library, we developed a complete end-to-end parallel electromagnetics code for computing the scattered electromagnetic fields from a Perfect Electrically Conducting surface. We used the functions provided by the software library to develop a Fast Multipole Method based solution to this problem. Experimental results show that our algorithms scale well and have bounded communication irrespective of the shape of the scatterer

A computational study of surface topography arising from energetic particle interactions

A computational investigation into the development of surface topographies subjected to energetic particle bombardment has been undertaken. Classical Molecular Dynamics (MD) and on-the- y kinetic Monte Carlo (otfKMC) techniques were employed and di erent bombardment conditions were considered. Surface topography development is of interest due to applications such as ion etching, which can be used in the manufacture of semiconductor devices. Crater formation on a HfO2-MgO interface system was investigated using a variety of methods. Initially single atom and cluster bombardments were performed, highlighting the radiation tolerance of the interface system. Subsequently, swift heavy ion bombardment of the interface was considered using a MD thermal spike model and an electron stripping with recombination model. Both models gave similar results to those seen experimentally: hillocks forming on the surfaces over the impact points of the ions; and ion tracks forming around the paths of the ions in the material. Hillock heights and sputtering yields were shown to increase linearly with the electronic stopping force of the bombarding ion, for the range of systems we considered. Bullet impacts on armour plating (SiC) have been simulated using MD. The bullet was modelled by a hard sphere that was forced into the substrate to the target depth. Both 4H and 6H SiC polytypes were considered with di erent bullet sizes and speeds. The 4H system resulted in the displacement of less atoms and also a much lower sputtering yield than for the similar 6H system. However dislocations were seen to propagate through the 4H system but not the 6H one. A large amount of sputtering was observed in the higher speed 6H simulations, with the ejection of many big clusters of atoms. These clusters generally had a high temperature (around 1,500 K) with speeds typically in excess of 1,000 m/s. Surface topography development by way of multiple impacts on Au was investigated using two di erent methodologies. Initially a traditional, MD based, methodology was used to model Au self bombardment of the high index f3 11 0g surface, which has been shown to produce interesting features. The disadvantage of this type of method is that MD cannot simulate time scales long enough to allow di usion between impacts. The MD method was shown to lead to a build up of defects in the systems: a result of the artificially high dose rate. An improved method was then used to model Ar and Au bombardment of both f0 1 0g and f3 11 0g Au surfaces. This hybrid MD-otfKMC technique enabled realistic time scales to be achieved. MD was used to model the ballistic phase while otfKMC was used to model di usion between events. The erosion rate of the surface was shown to be almost linear with time while the roughness of the surface was shown to oscillate: indicative of the healing process that occurs between bombardment events