A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.Comment: preprint, draft, 2 tables, 47 references, 7 files, Codes that can solve three dimensional linear elastostatic problems using constant boundary elements (of triangular shape) while ignoring body forces are provided as supplementary files; codes are distributed under the MIT License in three versions: i) MATLAB version ii) Fortran 90 version (sequential code) iii) Fortran 90 version (parallel code

Veamy: an extensible object-oriented C++ library for the virtual element method

This paper summarizes the development of Veamy, an object-oriented C++ library for the virtual element method (VEM) on general polygonal meshes, whose modular design is focused on its extensibility. The linear elastostatic and Poisson problems in two dimensions have been chosen as the starting stage for the development of this library. The theory of the VEM, upon which Veamy is built, is presented using a notation and a terminology that resemble the language of the finite element method (FEM) in engineering analysis. Several examples are provided to demonstrate the usage of Veamy, and in particular, one of them features the interaction between Veamy and the polygonal mesh generator PolyMesher. A computational performance comparison between VEM and FEM is also conducted. Veamy is free and open source software

Accurate computation of Galerkin double surface integrals in the 3-D boundary element method

Many boundary element integral equation kernels are based on the Green's functions of the Laplace and Helmholtz equations in three dimensions. These include, for example, the Laplace, Helmholtz, elasticity, Stokes, and Maxwell's equations. Integral equation formulations lead to more compact, but dense linear systems. These dense systems are often solved iteratively via Krylov subspace methods, which may be accelerated via the fast multipole method. There are advantages to Galerkin formulations for such integral equations, as they treat problems associated with kernel singularity, and lead to symmetric and better conditioned matrices. However, the Galerkin method requires each entry in the system matrix to be created via the computation of a double surface integral over one or more pairs of triangles. There are a number of semi-analytical methods to treat these integrals, which all have some issues, and are discussed in this paper. We present novel methods to compute all the integrals that arise in Galerkin formulations involving kernels based on the Laplace and Helmholtz Green's functions to any specified accuracy. Integrals involving completely geometrically separated triangles are non-singular and are computed using a technique based on spherical harmonics and multipole expansions and translations, which results in the integration of polynomial functions over the triangles. Integrals involving cases where the triangles have common vertices, edges, or are coincident are treated via scaling and symmetry arguments, combined with automatic recursive geometric decomposition of the integrals. Example results are presented, and the developed software is available as open source

A collocated C0 finite element method: Reduced quadrature perspective, cost comparison with standard finite elements, and explicit structural dynamics

We demonstrate the potential of collocation methods for efficient higher-order analysis on standard nodal finite element meshes. We focus on a collocation method that is variationally consistent and geometrically flexible, converges optimally, embraces concepts of reduced quadrature, and leads to symmetric stiffness and diagonal consistent mass matrices. At the same time, it minimizes the evaluation cost per quadrature point, thus reducing formation and assembly effort significantly with respect to standard Galerkin finite element methods. We provide a detailed review of all components of the technology in the context of elastodynamics, that is, weighted residual formulation, nodal basis functions on Gauss–Lobatto quadrature points, and symmetrization by averaging with the ultra-weak formulation. We quantify potential gains by comparing the computational efficiency of collocated and standard finite elements in terms of basic operation counts and timings. Our results show that collocation is significantly less expensive for problems dominated by the formation and assembly effort, such as higher-order elastostatic analysis. Furthermore, we illustrate the potential of collocation for efficient higher-order explicit dynamics. Throughout this work, we advocate a straightforward implementation based on simple modifications of standard finite element codes. We also point out the close connection to spectral element methods, where many of the key ideas are already established

A one point integration rule over star convex polytopes

In this paper, the recently proposed linearly consistent one point integration rule for the meshfree methods is extended to arbitrary polytopes. The salient feature of the proposed technique is that it requires only one integration point within each n-sided polytope as opposed to 3n in Francis et al. (2017) and 13n integration points in the conventional approach for numerically integrating the weak form in two dimensions. The essence of the proposed technique is to approximate the compatible strain by a linear smoothing function and evaluate the smoothed nodal derivatives by the discrete form of the divergence theorem at the geometric center. This is done by Taylor's expansion of the weak form which facilitates the use of the smoothed nodal derivatives acting as the stabilization term. This translates to 50% and 30% reduction in the overall computational time in the two and three dimensions, respectively, whilst preserving the accuracy and the convergence rates. Th

Numerical Computation of approximate Generalized Polarization Tensors

In this paper we describe a method to compute Generalized Polarization Tensors. These tensors are the coefficients appearing in the multipolar expansion of the steady state voltage perturbation caused by an inhomogeneity of constant conductivity. As an alternative to the integral equation approach, we propose an approximate semi-algebraic method which is easy to implement. This method has been integrated in a Myriapole, a matlab routine with a graphical interface which makes such computations available to non-numerical analysts