Developing Efficient High-Order Transport Schemes for Cross-Scale Coupled Estuary-Ocean Modeling

Geophysical fluid dynamics (GFD) models have progressed greatly in simulating the world’s oceans and estuaries in the past three decades, thanks to the development of novel numerical algorithms and the advent of massively parallel high-performance computing platforms. Study of inter-related processes on multi-scales (e.g., between large-scale (remote) processes and small-scale (local) processes) has always been an important theme for GFD modeling. For this purpose, models based on unstructured-grid (UG) have shown great potential because of their superior abilities in enabling multi-resolution and in fitting geometry and boundary. Despite UG models’ successful applications on coastal systems, significant obstacles still exist that have so far prevented UG models from realizing their full cross-scale capability. The pressing issues include the computation overhead resulting from large contrasts in the spatial resolutions, and the relative lack of skill for UG model in the eddying regime. Specifically for our own implicit UG model (SCHISM), the transport solver often emerges as a major bottleneck for both accuracy and efficiency. The overall goal of this dissertation is two-fold. The first goal is to address the challenges in tracer transport by developing efficient high-order schemes for the transport processes and test them in the framework of a community supported modeling system (SCHISM: Semi-implicit Cross-scale Hydroscience Integrated System Model) for cross-scale processes. The second goal is to utilize the new schemes developed in this dissertation and elsewhere to build a bona fide cross-scale Chesapeake Bay model and use it to address some key knowledge gaps in the physical processes in this system and to better assist decision makers of coastal resource management. The work on numerical scheme development has resulted in two new high-order transport solvers. The first solver tackles the vertical transport that often imposes the most stringent constraint on model efficiency (Chapter 2). With an implicit method and two flux limiters in both space and time, the new TVD2 solver leads to a speed-up of 1.6-6.0 in various cross-scale applications as compared to traditional explicit methods, while achieving 2nd-order accuracy in both space and time. Together with a flexible vertical gridding system, the flow over steep slopes can be faithfully simulated efficiently and accurately without altering the underlying bathymetry. The second scheme aims at improving the model skill in the eddying ocean (Chapter 4). UG coastal models tend to under-resolve features like meso-scale eddies and meanders, and this issue is partially attributed to the numerical diffusion in the transport schemes that are originally developed for estuarine applications. to address this issue, a 3rd-order transport scheme based on WENO formulation is developed, and is demonstrated to improve the meso-scale features. The new solvers are then tested in the Chesapeake Bay and adjacent Atlantic Ocean on small, medium and large domains respectively, corresponding to the three main chapters of this dissertation (Chapter 2-4), with an ultimate goal of achieving a seamless cross-scale model from the Gulf Stream to the shallow regions in the Bay tributaries and sub-tributaries. We highlight the dominant role played by the bathymetry in nearshore systems and the detrimental effects of bathymetric smoothing commonly used in many coastal models (Chapter 3). With the new methods developed in this dissertation and elsewhere, the model has enabled the analyses on some important processes that are hard to quantify with traditional techniques, e.g., the effect of channel-shoal contrast on lateral circulation and salinity distribution, hypoxia volume, the influence of realistic bathymetry on the freshwater plume etc. Potential topics for future research are also discussed at the end. In addition, the new solvers have also been successfully exported to many other oceanic and nearshore systems around the world via user groups of our community modeling system (cf. ‘Publications’ under ‘schism.wiki’)

The fourier virtual fields method for the identification of material property distributions

The requirement of a fast and accurate modulus identification technique has arisen in many fields of research, such as solid mechanics, structural health monitoring, medical diagnosis, etc. An inverse technique based on an appropriate interpretation of the principle of virtual work, namely the Virtual Fields Method (VFM), has been proposed in the literature, which is able to return elastic modulus values after a single matrix inversion. An extension of the virtual fields method to the spatial frequency domain in order to determine modulus distributions of materials based on a sine/cosine parameterisation of the unknown modulus is developed in this thesis, and will be called the Fourier-series-based Virtual Fields Method (F-VFM). The technique accepts in-plane (two-dimensional) or volumetric (three-dimensional) deformation measurement data as its input. An efficient numerical algorithm of the F-VFM based on the fast Fourier transform is presented, which can return thousands of unknown Fourier coefficients within a minute thus reducing the computation time by several orders of magnitude compared to a direct implementation of the F-VFM for typical dataset sizes. The F-VFM technique is also adapted to cope with a common situation in experimental mechanics where the knowledge of the boundary conditions is limited. The three versions of the F-VFM in this situation are respectively the experimental traction , windowed traction and Fourier-series traction approaches. The technique is then validated with numerical data from different stiffness patterns. The performance is compared to that of an iterative updating technique based on a genetic algorithm for one of these patterns, and computational effort is demonstrated to be at least five orders of magnitude less for the new F-VFM than for this updating method. The sensitivity of the performance of the F-VFM to noise is also investigated. Finally, the technique is applied to experimental data in both 2-D and 3-D cases with promising results

Doctor of Philosophy

dissertationRadiation is the dominant mode of heat transfer in high temperature combustion environments. Radiative heat transfer affects the gas and particle phases, including all the associated combustion chemistry. The radiative properties are in turn affected by the turbulent flow field. This bi-directional coupling of radiation turbulence interactions poses a major challenge in creating parallel-capable, high-fidelity combustion simulations. In this work, a new model was developed in which reciprocal monte carlo radiation was coupled with a turbulent, large-eddy simulation combustion model. A technique wherein domain patches are stitched together was implemented to allow for scalable parallelism. The combustion model runs in parallel on a decomposed domain. The radiation model runs in parallel on a recomposed domain. The recomposed domain is stored on each processor after information sharing of the decomposed domain is handled via the message passing interface. Verification and validation testing of the new radiation model were favorable. Strong scaling analyses were performed on the Ember cluster and the Titan cluster for the CPU-radiation model and GPU-radiation model, respectively. The model demonstrated strong scaling to over 1,700 and 16,000 processing cores on Ember and Titan, respectively

MECHANISTIC STUDIES OF THE COMPLETE ELECTROCHEMICAL OXIDATION OF ETHANOL INTO CO2 OVER PLATINUM-BASED CORE-SHELL NANOCATALYSTS

Direct ethanol fuel cells (DEFCs) are a promising technology for the generation of electricity via the direct conversion of ethanol into CO2, showing higher thermodynamic efficiency and volumetric energy density than hydrogen fuel cells. However, implementation of DEFCs is hampered by low selectivity of CO2 generation at the anode where the ethanol oxidation reaction (EOR) happens. Therefore, anode catalysts with high reactivity for the EOR and high selectivity for CO2 generation via breaking C-C bond are highly needed. To evaluate the catalysts’ capability of splitting C-C bond of the ethanol molecule, highly sensitive CO2 detection technique was developed in this research using a CO2 microelectrode. Such an in situ CO2 measurement tool enabled the real time detection of the partial pressure of CO2 during the EOR using linear sweeping voltammetry measurements, through which electro-kinetic details of CO2 generation could be obtained. Electro-kinetics of CO2 generation were studied on the PtRh/SnO2 core-shell catalysts made by a ‘surfactant-free’ method. The results showed that Pt and Rh components located in the core were partially oxidized and therefore improved the CO2 generation at low electrical potential. In addition, in situ CO2 measurements provided the mechanistic understanding of potentiodynamics of the EOR, particularly the influence of *OH adsorbates on CO2 generation rate and CO2 selectivity. Our results showed that at low potential, inadequate *OH adsorbates impaired the removal of reaction intermediates, and thus Pt/Rh/SnO2 exhibited the best performance toward CO2 generation due to its strong ability to dissociate water molecules forming *OH oxidants, while at high potential, Rh sites were overwhelmingly occupied (poisoned) by *OH adsorbates, and thus Pt/SnO2 exhibited the best performance toward CO2 generation

Numerical simulation of fracture pattern development and implications for fuid flow

Simulations are instrumental to understanding flow through discrete fracture geometric representations that capture the large-scale permeability structure of fractured porous media. The contribution of this thesis is threefold: an efficient finite-element finite-volume discretisation of the advection/diffusion flow equations, a geomechanical fracture propagation algorithm to create fractured rock analogues, and a study of the effect of growth on hydraulic conductivity. We describe an iterative geomechanics-based finite-element model to simulate quasi-static crack propagation in a linear elastic matrix from an initial set of random flaws. The cornerstones are a failure and propagation criterion as well as a geometric kernel for dynamic shape housekeeping and automatic remeshing. Two-dimensional patterns exhibit connectivity, spacing, and density distributions reproducing en echelon crack linkage, tip hooking, and polygonal shrinkage forms. Differential stresses at the boundaries yield fracture curving. A stress field study shows that curvature can be suppressed by layer interaction effects. Our method is appropriate to model layered media where interaction with neighbouring layers does not dominate deformation. Geomechanically generated fracture patterns are the input to single-phase flow simulations through fractures and matrix. Thus, results are applicable to fractured porous media in addition to crystalline rocks. Stress state and deformation history control emergent local fracture apertures. Results depend on the number of initial flaws, their initial random distribution, and the permeability of the matrix. Straightpath fracture pattern simplifications yield a lower effective permeability in comparison to their curved counterparts. Fixed apertures overestimate the conductivity of the rock by up to six orders of magnitude. Local sample percolation effects are representative of the entire model flow behaviour for geomechanical apertures. Effective permeability in fracture dataset subregions are higher than the overall conductivity of the system. The presented methodology captures emerging patterns due to evolving geometric and flow properties essential to the realistic simulation of subsurface processes

Analysis and Generation of Quality Polytopal Meshes with Applications to the Virtual Element Method

This thesis explores the concept of the quality of a mesh, the latter being intended as the discretization of a two- or three- dimensional domain. The topic is interdisciplinary in nature, as meshes are massively used in several fields from both the geometry processing and the numerical analysis communities. The goal is to produce a mesh with good geometrical properties and the lowest possible number of elements, able to produce results in a target range of accuracy. In other words, a good quality mesh that is also cheap to handle, overcoming the typical trade-off between quality and computational cost. To reach this goal, we first need to answer the question: ''How, and how much, does the accuracy of a numerical simulation or a scientific computation (e.g., rendering, printing, modeling operations) depend on the particular mesh adopted to model the problem? And which geometrical features of the mesh most influence the result?'' We present a comparative study of the different mesh types, mesh generation techniques, and mesh quality measures currently available in the literature related to both engineering and computer graphics applications. This analysis leads to the precise definition of the notion of quality for a mesh, in the particular context of numerical simulations of partial differential equations with the virtual element method, and the consequent construction of criteria to determine and optimize the quality of a given mesh. Our main contribution consists in a new mesh quality indicator for polytopal meshes, able to predict the performance of the virtual element method over a particular mesh before running the simulation. Strictly related to this, we also define a quality agglomeration algorithm that optimizes the quality of a mesh by wisely agglomerating groups of neighboring elements. The accuracy and the reliability of both tools are thoroughly verified in a series of tests in different scenarios

Innovative Approaches to 3D GIS Modeling for Volumetric and Geoprocessing Applications in Subsurface Infrastructures in a Virtual Immersive Environment

As subsurface features remain largely ‘out of sight, out of mind’, this has led to challenges when dealing with underground space and infrastructures and especially so for those working in GIS. Since subsurface infrastructure plays a major role in supporting the needs of modern society, groups such as city planners and utility companies and decision makers are looking for an ‘holistic’ approach where the sustainable use of underground space is as important as above ground space. For such planning and management, it is crucial to examine subsurface data in a form that is amenable to 3D mapping and that can be used for increasingly sophisticated 3D modeling. The subsurface referred to in this study focuses particularly on examples of both shallow and deep underground infrastructures. In the case of shallow underground infrastructures mostly two-dimensional maps are used in the management and planning of these features. Depth is a very critical component of underground infrastructures that is difficult to represent in a 2D map and for this reason these are best studied in three-dimensional space. In this research, the capability of 3D GIS technology and immersive geography are explored for the storage, management, analysis, and visualization of shallow and deep subsurface features