Statistical Effective Diffusivity Estimation in Porous Media Using an Integrated On-site Imaging Workflow for Synchrotron Users

Transport in porous media plays an essential role for many physical, engineering, biological and environmental processes. Novel synchrotron imaging techniques and image-based models have enabled more robust quantification of geometric structures that influence transport through the pore space. However, image-based modelling is computationally expensive, and end users often require, while conducting imaging campaign, fast and agile bulk-scale effective parameter estimates that account for the pore-scale details. In this manuscript we enhance a pre-existing image-based model solver known as OpenImpala to estimate bulk-scale effective transport parameters. In particular, the boundary conditions and equations in OpenImpala were modified in order to estimate the effective diffusivity in an imaged system/geometry via a formal multi-scale homogenisation expansion. Estimates of effective pore space diffusivity were generated for a range of elementary volume sizes to estimate when the effective diffusivity values begin to converge to a single value. Results from OpenImpala were validated against a commercial finite element method package COMSOL Multiphysics (abbreviated as COMSOL). Results showed that the effective diffusivity values determined with OpenImpala were similar to those estimated by COMSOL. Tests on larger domains comparing a full image-based model to a homogenised (geometrically uniform) domain that used the effective diffusivity parameters showed differences below 2 % error, thus verifying the accuracy of the effective diffusivity estimates. Finally, we compared OpenImpala’s parallel computing speeds to COMSOL. OpenImpala consistently ran simulations within fractions of minutes, which was two orders of magnitude faster than COMSOL providing identical supercomputing specifications. In conclusion, we demonstrated OpenImpala’s utility as part of an on-site tomography processing pipeline allowing for fast and agile assessment of porous media processes and to guide imaging campaigns while they are happening at synchrotron beamlines

Image-based Modeling of Flow through Porous Media: Development of Multiscale Techniques for the Pore Level

Increasingly, imaging technology allows porous media problems to be modeled at microscopic and sub-microscopic levels with finer resolution. However, the physical domain size required to be representative of the media prohibits comprehensive micro-scale simulation. A hybrid or multiscale approach is necessary to overcome this challenge. In this work, a technique was developed for determining the characteristic scales of porous materials, and a multiscale modeling methodology was developed to better understand the interaction/dependence of phenomena occurring at different microscopic scales. The multiscale method couples microscopic simulations at the pore and sub-pore scales. Network modeling is a common pore-scale technique which employs severe assumptions, making it more computationally efficient than direct numerical simulation, enabling simulation over larger length scales. However, microscopic features of the medium are lost in the discretization of a material into a network of interconnected pores and throats. In contrast, detailed microstructure and flow patterns can be captured by modern meshing and direct numerical simulation techniques, but these models are computationally expensive. In this study, a data-driven multiscale technique has been developed that couples the two types of models, taking advantage of the benefits of each. Specifically, an image-based physically-representative pore network model is coupled to an FEM (finite element method) solver that operates on unstructured meshes capable of resolving details orders of magnitude smaller than the pore size. In addition to allowing simulation at multiple scales, the current implementation couples the models using a machine learning approach, where results from the FEM model are used to learn network model parameters. Examples of the model operating on real materials are given that demonstrate improvements in network modeling enabled by the multiscale framework. The framework enables more advanced multiscale and multiphysics modeling – an application to particle straining problems is shown. More realistic network filtration simulations are possible by incorporating information from the sub-pore-scale. New insights into the size exclusion mechanism of particulate filtration were gained in the process of generating data for machine learning of conductivity reduction due to particle trapping. Additional tests are required to validate the multiscale network filtration model, and compare with experimental findings in literature

Finite Element Modeling Driven by Health Care and Aerospace Applications

This thesis concerns the development, analysis, and computer implementation of mesh generation algorithms encountered in finite element modeling in health care and aerospace. The finite element method can reduce a continuous system to a discrete idealization that can be solved in the same manner as a discrete system, provided the continuum is discretized into a finite number of simple geometric shapes (e.g., triangles in two dimensions or tetrahedrons in three dimensions). In health care, namely anatomic modeling, a discretization of the biological object is essential to compute tissue deformation for physics-based simulations. This thesis proposes an efficient procedure to convert 3-dimensional imaging data into adaptive lattice-based discretizations of well-shaped tetrahedra or mixed elements (i.e., tetrahedra, pentahedra and hexahedra). This method operates directly on segmented images, thus skipping a surface reconstruction that is required by traditional Computer-Aided Design (CAD)-based meshing techniques and is convoluted, especially in complex anatomic geometries. Our approach utilizes proper mesh gradation and tissue-specific multi-resolution, without sacrificing the fidelity and while maintaining a smooth surface to reflect a certain degree of visual reality. Image-to-mesh conversion can facilitate accurate computational modeling for biomechanical registration of Magnetic Resonance Imaging (MRI) in image-guided neurosurgery. Neuronavigation with deformable registration of preoperative MRI to intraoperative MRI allows the surgeon to view the location of surgical tools relative to the preoperative anatomical (MRI) or functional data (DT-MRI, fMRI), thereby avoiding damage to eloquent areas during tumor resection. This thesis presents a deformable registration framework that utilizes multi-tissue mesh adaptation to map preoperative MRI to intraoperative MRI of patients who have undergone a brain tumor resection. Our enhancements with mesh adaptation improve the accuracy of the registration by more than 5 times compared to rigid and traditional physics-based non-rigid registration, and by more than 4 times compared to publicly available B-Spline interpolation methods. The adaptive framework is parallelized for shared memory multiprocessor architectures. Performance analysis shows that this method could be applied, on average, in less than two minutes, achieving desirable speed for use in a clinical setting. The last part of this thesis focuses on finite element modeling of CAD data. This is an integral part of the design and optimization of components and assemblies in industry. We propose a new parallel mesh generator for efficient tetrahedralization of piecewise linear complex domains in aerospace. CAD-based meshing algorithms typically improve the shape of the elements in a post-processing step due to high complexity and cost of the operations involved. On the contrary, our method optimizes the shape of the elements throughout the generation process to obtain a maximum quality and utilizes high performance computing to reduce the overheads and improve end-user productivity. The proposed mesh generation technique is a combination of Advancing Front type point placement, direct point insertion, and parallel multi-threaded connectivity optimization schemes. The mesh optimization is based on a speculative (optimistic) approach that has been proven to perform well on hardware-shared memory. The experimental evaluation indicates that the high quality and performance attributes of this method see substantial improvement over existing state-of-the-art unstructured grid technology currently incorporated in several commercial systems. The proposed mesh generator will be part of an Extreme-Scale Anisotropic Mesh Generation Environment to meet industries expectations and NASA\u27s CFD visio

Brain and Human Body Modeling

This open access book describes modern applications of computational human modeling with specific emphasis in the areas of neurology and neuroelectromagnetics, depression and cancer treatments, radio-frequency studies and wireless communications. Special consideration is also given to the use of human modeling to the computational assessment of relevant regulatory and safety requirements. Readers working on applications that may expose human subjects to electromagnetic radiation will benefit from this book’s coverage of the latest developments in computational modelling and human phantom development to assess a given technology’s safety and efficacy in a timely manner. Describes construction and application of computational human models including anatomically detailed and subject specific models; Explains new practices in computational human modeling for neuroelectromagnetics, electromagnetic safety, and exposure evaluations; Includes a survey of modern applications for which computational human models are critical; Describes cellular-level interactions between the human body and electromagnetic fields

A Multi-Core Numerical Framework for Characterizing Flow in Oil Reservoirs

Presented at the SCS Spring Simulation Multi-Conference – SpringSim 2011, April 4-7, 2011 – Boston, USA Awarded Best Paper in the 19th High Performance Computing Symposium and Best Overall Paper at SpringSim 2011.This paper presents a numerical framework that enables scalable, parallel execution of engineering simulations on multi-core, shared memory architectures. Distribution of the simulations is done by selective hash-tabling of the model domain which spatially decomposes it into a number of orthogonal computational tasks. These tasks, the size of which is critical to optimal cache blocking and consequently performance, are then distributed for execution to multiple threads using the previously presented task management algorithm, H-Dispatch. Two numerical methods, smoothed particle hydrodynamics (SPH) and the lattice Boltzmann method (LBM), are discussed in the present work, although the framework is general enough to be used with any explicit time integration scheme. The implementation of both SPH and the LBM within the parallel framework is outlined, and the performance of each is presented in terms of speed-up and efficiency. On the 24-core server used in this research, near linear scalability was achieved for both numerical methods with utilization efficiencies up to 95%. To close, the framework is employed to simulate fluid flow in a porous rock specimen, which is of broad geophysical significance, particularly in enhanced oil recovery

Numerical studies of flow in porous media using an unstructured approach

Flow and transport in porous media is relevant to many areas of engineering and science including groundwater hydrology and the recovery of oil and gas. Porous materials are characterized by the unique shape and connectivity of the internal void structures which give rise to a large range in macroscopic transport properties. Historically an inability to accurately describe the internal pore-structure has prevented detailed study of the role of pore structure on transport. In recent decades however, the combination of high resolution imaging technologies with computational modeling has seen the development of fundamental pore-scale techniques for studying flow in porous media. Image-based pore-scale modeling of transport phenomena has become an important tool for understanding the complicated relationships between pore structure and measurable macroscopic properties, including permeability and formation factor. This has commonly been achieved by a network-based approach where the pore space is idealized as a series of pores connected by throats, or by a grid-based approach where the voxels of a 3D image represent structured quadrilateral elements or nodal locations. In this work however, image-based unstructured meshing techniques are used to represent voxelised pore spaces by grids comprising entirely of tetrahedral elements. These unstructured tetrahedral grids are used in finite element models to calculate permeability and formation factor. Solutions to the Stokes equations governing creeping, or Darcy flow, are used to validate the finite element approach employed in this work, and to assess the impact of different image-based unstructured meshing strategies on predicted permeability. Testing shows that solutions to the Stokes equations by a P2P1 tetrahedral element are significantly more accurate than solutions based on a P1P1 element, while permeability is shown to be sensitive to structural changes to the pore space induced by different meshing approaches. The modeling approach is also used to investigate the relationship of an electric and hydraulic definition of tortuosity to the Carman-Kozeny equation. The results of simulations using a number of computer generated porous structures indicate that an electrical tortuosity based on computed formation factor is well correlated with the tortuosity suggested by the Carman-Kozeny equation

Scan-based immersed isogeometric analysis

Scan-based simulations contain innate topologically complex three-dimensional geometries, represented by large data sets in formats which are not directly suitable for analysis. Consequently, performing high-fidelity scan-based simulations at practical computational costs is still very challenging. The main objective of this dissertation is to develop an efficient and robust scan-based simulation strategy by acquiring a profound understanding of three prominent challenges in scan-based IGA, viz.: i) balancing the accuracy and computational effort associated with numerical integration; ii) the preservation of topology in the spline-based segmentation procedure; and iii) the control of accuracy using error estimation and adaptivity techniques. In three-dimensional immersed isogeometric simulations, the computational effort associated with integration can be the critical component. A myriad of integration strategies has been proposed over the past years to ameliorate the difficulties associated with integration, but a general optimal integration framework that suits a broad class of engineering problems is not yet available. In this dissertation we provide a thorough investigation of the accuracy and computational effort of the octree integration technique. We quantify the contribution of the integration error using the theoretical basis provided by Strang’s first lemma. Based on this study we propose an error-estimate-based adaptive integration procedure for immersed IGA. To exploit the advantageous properties of IGA in a scan-based setting, it is important to extract a smooth geometry. This can be established by convoluting the voxel data using B-splines, but this can induce problematic topological changes when features with a size similar to that of the voxels are encountered. This dissertation presents a topology-preserving segmentation procedure using truncated hierarchical (TH)B-splines. A moving-window-based topological anomaly detection algorithm is proposed to identify regions in which (TH)B-spline refinements must be performed. The criterion to identify topological anomalies is based on the Euler characteristic, giving it the capability to distinguish between topological and shape changes. A Fourier analysis is presented to explain the effectiveness of the developed procedure. An additional computational challenge in the context of immersed IGA is the construction of optimal approximations using locally refined splines. For scan-based volumetric domains, hierarchical splines are particularly suitable, as they optimally leverage the advantages offered by the availability of a geometrically simple background mesh. Although truncated hierarchical B-splines have been successfully applied in the context of IGA, their application in the immersed setting is largely unexplored. In this dissertation we propose a computational strategy for the application of error estimation-based mesh adaptivity for stabilized immersed IGA. The conducted analyses and developed computational techniques for scan-based immersed IGA are interrelated, and together constitute a significant improvement in the efficiency and robustness of the analysis paradigm. In combination with other state-of-the-art developments regarding immersed FEM/IGA (\emph{e.g.}, iterative solution techniques, parallel computing), the research in this thesis opens the doors to scan-based simulations with more sophisticated physical behavior, geometries of increased complexity, and larger scan-data sizes.Scan-based simulations contain innate topologically complex three-dimensional geometries, represented by large data sets in formats which are not directly suitable for analysis. Consequently, performing high-fidelity scan-based simulations at practical computational costs is still very challenging. The main objective of this dissertation is to develop an efficient and robust scan-based simulation strategy by acquiring a profound understanding of three prominent challenges in scan-based IGA, viz.: i) balancing the accuracy and computational effort associated with numerical integration; ii) the preservation of topology in the spline-based segmentation procedure; and iii) the control of accuracy using error estimation and adaptivity techniques. In three-dimensional immersed isogeometric simulations, the computational effort associated with integration can be the critical component. A myriad of integration strategies has been proposed over the past years to ameliorate the difficulties associated with integration, but a general optimal integration framework that suits a broad class of engineering problems is not yet available. In this dissertation we provide a thorough investigation of the accuracy and computational effort of the octree integration technique. We quantify the contribution of the integration error using the theoretical basis provided by Strang’s first lemma. Based on this study we propose an error-estimate-based adaptive integration procedure for immersed IGA. To exploit the advantageous properties of IGA in a scan-based setting, it is important to extract a smooth geometry. This can be established by convoluting the voxel data using B-splines, but this can induce problematic topological changes when features with a size similar to that of the voxels are encountered. This dissertation presents a topology-preserving segmentation procedure using truncated hierarchical (TH)B-splines. A moving-window-based topological anomaly detection algorithm is proposed to identify regions in which (TH)B-spline refinements must be performed. The criterion to identify topological anomalies is based on the Euler characteristic, giving it the capability to distinguish between topological and shape changes. A Fourier analysis is presented to explain the effectiveness of the developed procedure. An additional computational challenge in the context of immersed IGA is the construction of optimal approximations using locally refined splines. For scan-based volumetric domains, hierarchical splines are particularly suitable, as they optimally leverage the advantages offered by the availability of a geometrically simple background mesh. Although truncated hierarchical B-splines have been successfully applied in the context of IGA, their application in the immersed setting is largely unexplored. In this dissertation we propose a computational strategy for the application of error estimation-based mesh adaptivity for stabilized immersed IGA. The conducted analyses and developed computational techniques for scan-based immersed IGA are interrelated, and together constitute a significant improvement in the efficiency and robustness of the analysis paradigm. In combination with other state-of-the-art developments regarding immersed FEM/IGA (\emph{e.g.}, iterative solution techniques, parallel computing), the research in this thesis opens the doors to scan-based simulations with more sophisticated physical behavior, geometries of increased complexity, and larger scan-data sizes

Brain and Human Body Modeling

This open access book describes modern applications of computational human modeling with specific emphasis in the areas of neurology and neuroelectromagnetics, depression and cancer treatments, radio-frequency studies and wireless communications. Special consideration is also given to the use of human modeling to the computational assessment of relevant regulatory and safety requirements. Readers working on applications that may expose human subjects to electromagnetic radiation will benefit from this book’s coverage of the latest developments in computational modelling and human phantom development to assess a given technology’s safety and efficacy in a timely manner. Describes construction and application of computational human models including anatomically detailed and subject specific models; Explains new practices in computational human modeling for neuroelectromagnetics, electromagnetic safety, and exposure evaluations; Includes a survey of modern applications for which computational human models are critical; Describes cellular-level interactions between the human body and electromagnetic fields

An explicit stabilised finite element method for Navier-Stokes-Brinkman equations

We present an explicit stabilised finite element method for solving Navier-Stokes-Brinkman equations. The proposed algorithm has several advantages. First, the lower equal-order finite element space for velocity and pressure is ideal for presenting the pixel images. Stabilised finite element allows the continuity of both tangential and normal velocities at the interface between regions of different micro-permeability or at the interface free/porous domain. Second, the algorithm is fully explicit and versatile for describing complex boundary conditions. Third, the fully explicit matrix–free finite element implementation is ideal for parallelism on high-performance computers. In the last, the implicit treatment of Darcy term allowed larger time stepping and a stable computation, even if the velocity varies for several orders of magnitude in the micro-porous regions (Darcy regime). The stabilisation parameter, that may affect the velocity field, has been discussed and an optimal parameter was chosen based on the numerical examples. Velocity stability at interface between different micro-permeability has been also studied with mesh refinement. We analysed the influence of the micro-permeability field on the regime of the flow (Stokes flow, Darcy flow or a transitional regime). These benchmark tests provide guidelines for choosing the resolution of the grayscale image and its segmentation. We applied the method on real Berea Sandstone micro-CT images, and proceeded the three-phases segmentation. We studied the influence of the micro-porosity field, using the well-known Kozeny-Carman relation to derive the micro-permeability field from the micro-porosity field, on the effective permeability computed. Our analysis shows that a small fraction of micro-porosity in the rock has a significant influence on the effective permeability computed