Nanostructure Modeling in Oxide Ceramics Using Large Scale Parallel Molecular Dynamics Simulations.

The purpose of this dissertation is to investigate the properties and processes in nanostructured oxide ceramics using molecular-dynamics (MD) simulations. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. The dynamics of oxidation of aluminum nanoclusters is studied with a MD scheme that can simultaneously treat metallic and oxide systems. Dynamic charge transfer between anions and cations which gives rise to a compute-intensive Coulomb interaction, is treated by the O(N) Fast Multipole Method. Structural and dynamical correlations and local stresses reveal significant charge transfer and stress variations which cause rapid diffusion of Al and O on the nanocluster surface. At a constant temperature, the formation of an amorphous surface-oxide layer is observed during the first 100 picoseconds. Subsequent sharp decrease in O diffusion normal to the cluster surface arrests the growth of the oxide layer with a saturation thickness of 4 nanometers; this is in excellent agreement with experiments. Analyses of the oxide scale reveal significant charge transfer and variations in local structure. When the heat is not extracted from the cluster, the oxidizing reaction becomes explosive. Sintering, structural correlations, vibrational properties, and mechanical behavior of nanophase silica glasses are also studied using the MD approach based on an empirical interatomic potential that consists of both two and three-body interactions. Nanophase silica glasses with densities ranging from 76 to 93% of the bulk glass density are obtained using an isothermal-isobaric MD approach. During the sintering process, the pore sizes and distribution change without any discernable change in the pore morphology. The height and position of the first sharp diffraction peak (the signature of intermediate-range order) in the neutron static structure factor shows significant differences in the nanophase glasses relative to the bulk silica glass. Enhancement of the low-energy vibrational modes is observed. The effect of densification on mechanical properties is also examined

Multi-level load balancing for parallel particle simulations

Ideas from multi-level relaxation methods are combined with load balancing techniques to achieve a convergence acceleration for a homogeneous work load distribution over a given set of processors when the underlying work function is inhomogeneously distributed in space. The algorithm is based on an orthogonal recursive bisection ap- proach which is evaluated via a hierarchically refined coarse integration. The method only requires a minimal information transfer across processors during the tree traversal steps. It is described of how to partition the system of processors to geometrical space, when global information is needed for the spatial tesselation

Granite: A scientific database model and implementation

The principal goal of this research was to develop a formal comprehensive model for representing highly complex scientific data. An effective model should provide a conceptually uniform way to represent data and it should serve as a framework for the implementation of an efficient and easy-to-use software environment that implements the model. The dissertation work presented here describes such a model and its contributions to the field of scientific databases. In particular, the Granite model encompasses a wide variety of datatypes used across many disciplines of science and engineering today. It is unique in that it defines dataset geometry and topology as separate conceptual components of a scientific dataset. We provide a novel classification of geometries and topologies that has important practical implications for a scientific database implementation. The Granite model also offers integrated support for multiresolution and adaptive resolution data. Many of these ideas have been addressed by others, but no one has tried to bring them all together in a single comprehensive model. The datasource portion of the Granite model offers several further contributions. In addition to providing a convenient conceptual view of rectilinear data, it also supports multisource data. Data can be taken from various sources and combined into a unified view. The rod storage model is an abstraction for file storage that has proven an effective platform upon which to develop efficient access to storage. Our spatial prefetching technique is built upon the rod storage model, and demonstrates very significant improvement in access to scientific datasets, and also allows machines to access data that is far too large to fit in main memory. These improvements bring the extremely large datasets now being generated in many scientific fields into the realm of tractability for the ordinary researcher. We validated the feasibility and viability of the model by implementing a significant portion of it in the Granite system. Extensive performance evaluations of the implementation indicate that the features of the model can be provided in a user-friendly manner with an efficiency that is competitive with more ad hoc systems and more specialized application specific solutions

Scalable parallel molecular dynamics algorithms for organic systems

A scalable parallel algorithm, Macro-Molecular Dynamics (MMD), has been developed for large-scale molecular dynamics simulations of organic macromolecules, based on space-time multi-resolution techniques and dynamic management of distributed lists. The algorithm also includes the calculation of long range forces using Fast Multipole Method (FMM). FMM is based on the octree data structure, in which each parent cell is divided into 8 child cells and this division continues until the cell size is equal to the non-bonded interaction cutoff length. Due to constant number of operations performed at each stage of the octree, the FMM algorithm scales as O(N). Design and analysis of MMD and FMM algorithms are presented. Scalability tests are performed on three tera-flop machines: 1024-processor Intel Xeon-based Linux cluster, SuperMike at LSU, 1184-processor IBM SP4 Marcellus and the 512-processor Compaq AlphaServer Emerald at the U.S. Army Engineer Research and Development Center (ERDC) MSRC. The tests show that the Linux cluster outperforms the SP4 for the MMD application. The tests also show significant effects of memory- and cache-sharing on the performance

Multiresolution analysis of electronic structure: semicardinal and wavelet bases

This article reviews recent developments in multiresolution analysis which make it a powerful tool for the systematic treatment of the multiple length-scales inherent in the electronic structure of matter. Although the article focuses on electronic structure, the advances described are useful for non-linear problems in the physical sciences in general. The new language and notations introduced are well- suited for both formal manipulations and the development of computer software using higher-level languages such as C++. The discussion is self-contained, and all needed algorithms are specified explicitly in terms of simple operators and illustrated with straightforward diagrams which show the flow of data. Among the reviewed developments is the construction of_exact_ multiresolution representations from extremely limited samples of physical fields in real space. This new and profound result is the critical advance in finally allowing systematic, all electron calculations to compete in efficiency with state-of-the-art electronic structure calculations which depend for their celerity upon freezing the core electronic degrees of freedom. This review presents the theory of wavelets from a physical perspective, provides a unified and self-contained treatment of non-linear couplings and physical operators and introduces a modern framework for effective single-particle theories of quantum mechanics.Comment: A "how-to from-scratch" book presently in press at Reviews of Modern Physics: 88 pages, 31 figures, 5 tables, 88 references. Significantly IMPROVED version, including (a) new diagrams illustrating algorithms; (b) careful proof-reading of equations and text; (c) expanded bibliography; (d) cosmetic changes including lists of figures and tables and a more reasonable font. Latest changes (Dec. 11, 1998): a more descriptive abstract, and minor lexicographical change

Indium Arsenide/Gallium Arsenide Quantum Dots and Nanomesas: Multimillion-Atom Molecular Dynamics Solutions on Parallel Architectures.

Multimillion-atom molecular dynamics (MD) simulations have been performed to study the flat InAs overlayers with self-limiting thickness on GaAs square nanomesas. The in-plane lattice constant of InAs layers parallel to the InAs/GaAs(001) interface starts to exceed the InAs bulk value at 12th monolayer (ML) and the hydrostatic stresses in InAs layers become tensile above ∼12 th ML. As a result, it is not favorable to have InAs overlayers thicker than 12 ML. This may explain the experimental findings of the growth of flat InAs overlayers with self-limiting thickness of ∼11 ML on GaAs nanomesas. We have also examined the lateral size effects on the stress distribution and morphology of InAs/GaAs square nanomesas using parallel molecular dynamics. Two mesas with the same vertical size but different lateral sizes are simulated. For the smaller mesa, a single stress domain is observed in the InAs overlayer, whereas two stress domains are found in the larger mesa. This indicates the existence of a critical lateral size for domain formation in accordance with recent experimental findings. The InAs overlayer in the larger mesa is laterally constrained to the GaAs bulk lattice constant but vertically relaxed to the InAs bulk lattice constant, consistent with the Poisson effect. Moreover, we have calculated surface energies of GaAs and InAs for the (100), (110), and (111) orientations. Both MD and the conjugate gradient method are used and the results are in excellent agreement. Surface reconstructions on GaAs(100) and InAs(100) are studied via the conjugate gradient method. We have developed a new model for GaAs(100) and InAs(100) surface atoms. Not only this model reproduces well surface energies for the (100) orientation, it also yields (1 x 2) dimer lengths in accordance with Ab initio calculations. Finally, a series of molecular dynamics simulations are performed to investigate the behavior under load of several 〈001〉 and 〈011〉 symmetrical tilt grain boundaries (GBs) in diamond. These MD simulations are based on the bond-order analytic potential. Crack propagation in polycrystalline diamond samples under an applied load is simulated, and found to be predominantly transgranular rather than intergranular

Space-time adaptive resolution for reactive flows

Multi-scale systems evolve over a wide range of temporal and spatial scales. The extent of time scales makes both theoretical and numerical analysis difficult, mostly because the time scales of interest are typically much slower than the fastest scales occurring in the system. Systems with such characteristics are usually classified as being stiff. An adaptive mesh refinement method based on the wavelet transform and the G-Scheme framework are used to achieve spatial and temporal adaptive model reduction, respectively, of physical problems described by PDEs. The combination of the methods is proposed to solve PDEs describing reaction-diffusion systems with the minimal number of degrees of freedom, for prescribed accuracies in space and time. Different reaction-diffusion systems are studied with the aim to test the performance and the capability of the combined scheme to generate accurate solutions with respect to reference ones. Several strategies are implemented to improve the performance of the scheme, with minimal loss of accuracy

Institute for Computational Mechanics in Propulsion (ICOMP)

The Institute for Computational Mechanics in Propulsion (ICOMP) is a combined activity of Case Western Reserve University, Ohio Aerospace Institute (OAI) and NASA Lewis. The purpose of ICOMP is to develop techniques to improve problem solving capabilities in all aspects of computational mechanics related to propulsion. The activities at ICOMP during 1991 are described

Parallelization solutions for the YNANO Discontinua Simulations.

PhDIn the context of constant and fast progresses in nano technology, discontinua based computation simulations are becoming increasingly important, especially in the context of virtual experimentations. The efficiency of discontinua based nanoscale simulations are still limited by CPU capacity (the number of simulation particles in the system). It is accepted that parallelization will play an important role in solving this problem. In this thesis, two parallelization approaches have been undertaken to parallelize the YNANO discontinua simulations. The scope of the work includes parallelization of the YNANO using the shared-memory approach OpenMP and the distributed-memory approach MPI, and also includes a novel MR_PB linear contact detection algorithm which can be used under periodic boundary conditions. The developed MPI parallelization solutions are compatible with the MR linear contact detection algorithm used in the sequential YNANO, the developed solutions preserves the linearity of both MR_Sort and MR_Search algorithm. The overall performance and scalability of the parallelization has been studied using nanoscale simulations in fluid dynamics and aerodynamics