The Experts below are selected from a list of 7074 Experts worldwide ranked by ideXlab platform
Desheng Wang - One of the best experts on this subject based on the ideXlab platform.
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adaptive Tetrahedral Mesh generation by constrained centroidal voronoi delaunay tessellations for finite element methods
Numerical Methods for Partial Differential Equations, 2014Co-Authors: Jie Chen, Desheng Wang, Yunqing Huang, Xiaoping XieAbstract:This article presents a Tetrahedral Mesh adaptivity algorithm for three-dimensional elliptic partial differential equations (PDEs) using finite element methods. The main issues involved are the Mesh size and Mesh quality, which have great influence on the accuracy of the numerical solution and computational cost. The first issue is addressed by a posteriori error estimator based on superconvergent gradient recovery. The second issue is solved by constrained centroidal Voronoi–Delaunay tessellations (CCVDT), which guarantees good quality tetrahedrons over a large class of Mesh domains even, if the grid size varies a lot at any particular refinement level. The CCVDT enjoys the energy equidistribution property so that the errors are very well equidistributed with properly chosen sizing field (density function). And with this good property, a new refinement criteria is raised which is different from the traditional bisection refinement. © 2013 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 30: 1633–1653, 2014
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improvements in the reliability and element quality of parallel Tetrahedral Mesh generation
International Journal for Numerical Methods in Engineering, 2012Co-Authors: Jianjun Chen, Yao Zheng, Dawei Zhao, Zhengge Huang, Desheng WangAbstract:SUMMARY The paper presents a parallel Tetrahedral Mesh generation approach based on recursive bidivisions using triangular surfaces. Research was conducted for addressing issues concerning Mesh generation reliability and element quality. A novel procedure employing local modification techniques is proposed for repairing the intersecting interdomain Mesh instead of directly repeating the bidivision procedure, which improves the robustness of the complete Meshing procedure significantly. In addition, a new parallel quality improvement scheme is suggested for optimizing the distributed volume Meshes. The scheme is free of any communication cost and highly efficient. Finally, Mesh experiments of hundreds of millions of elements are performed to demonstrate the reliability, effectiveness and efficiency of the proposed method and its potential applications to large-scale simulations of complex aerodynamics models. Copyright © 2012 John Wiley & Sons, Ltd.
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Tetrahedral Mesh generation and optimization based on centroidal voronoi tessellations
International Journal for Numerical Methods in Engineering, 2003Co-Authors: Desheng WangAbstract:The centroidal Voronoi tessellation based Delaunay triangulation (CVDT) provides an optimal distribution of generating points with respect to a given density function and accordingly generates a high-quality Mesh. In this paper, we discuss algorithms for the construction of the constrained CVDT from an initial Delaunay Tetrahedral Mesh of a three-dimensional domain. By establishing an appropriate relationship between the density function and the specified sizing field and applying the Lloyd's iteration, the constrained CVDT Mesh is obtained as a natural global optimization of the initial Mesh. Simple local operations such as edges/faces flippings are also used to further improve the CVDT Mesh. Several complex Meshing examples and their element quality statistics are presented to demonstrate the effectiveness and efficiency of the proposed Mesh generation and optimization method. Copyright © 2003 John Wiley & Sons, Ltd.
Wei Shyy - One of the best experts on this subject based on the ideXlab platform.
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two step multi resolution reconstruction based compact gas kinetic scheme on Tetrahedral Mesh
arXiv: Computational Physics, 2021Co-Authors: Fengxiang Zhao, Wei ShyyAbstract:In this paper, a third-order compact gas-kinetic scheme (GKS) on unstructured Tetrahedral Mesh is constructed for the compressible Euler and Navier-Stokes solutions. The time-dependent gas distribution function at a cell interface is used to calculate the fluxes for the updating the cell-averaged flow variables and to evaluate the time accurate cell-averaged flow variables as well for evolving the cell-averaged gradients of flow variables. With the accurate evolution model for both flow variables and their slopes, the quality of the scheme depends closely on the accuracy and reliability of the initial reconstruction of flow variables. The reconstruction scheme becomes more challenge on Tetrahedral Mesh, where the conventional second-order unlimited least-square reconstruction can make the scheme be linearly unstable when using cell-averaged conservative variables alone with von Neumann neighbors. Benefiting from the evolved cell-averaged slopes, on Tetrahedral Mesh the GKS is linearly stable from a compact third-order smooth reconstruction with a large CFL number. In order to further increase the robustness of the high-order compact GKS for capturing discontinuous solution, a new two-step multi-resolution weighted essentially non-oscillatory (WENO) reconstruction will be proposed. The novelty of the reconstruction includes the following. Firstly, it releases the stability issue from a second-order compact reconstruction through the introduction of a pre-reconstruction step. Secondly, in the third-order non-linear reconstruction, only one more large stencil is added beside those in the second-order one, which significantly simplifies the high-order reconstruction. The proposed third-order scheme shows good robustness in high speed flow computation and favorable Mesh adaptability in cases with complex geometry.
Takuya Furuta - One of the best experts on this subject based on the ideXlab platform.
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paradim a phits based monte carlo tool for internal dosimetry with Tetrahedral Mesh computational phantoms
The Journal of Nuclear Medicine, 2019Co-Authors: Lukas M Carter, Chansoo Choi, Chan Hyeong Kim, Takuya Furuta, Tatsuhiko Sato, Justin L. Brown, Wesley E. Bolch, Troy Crawford, Pat ZanzonicoAbstract:Mesh-type and voxel-based computational phantoms comprise the current state of the art for internal dose assessment via Monte Carlo simulations but excel in different aspects, with Mesh-type phantoms offering advantages over their voxel counterparts in terms of their flexibility and realistic representation of detailed patient- or subject-specific anatomy. We have developed PARaDIM (pronounced "paradigm": Particle and Heavy Ion Transport Code System-Based Application for Radionuclide Dosimetry in Meshes), a freeware application for implementing Tetrahedral Mesh-type phantoms in absorbed dose calculations. It considers all medically relevant radionuclides, including α, β, γ, positron, and Auger/conversion electron emitters, and handles calculation of mean dose to individual regions, as well as 3-dimensional dose distributions for visualization and analysis in a variety of medical imaging software. This work describes the development of PARaDIM, documents the measures taken to test and validate its performance, and presents examples of its uses. Methods: Human, small-animal, and cell-level dose calculations were performed with PARaDIM and the results compared with those of widely accepted dosimetry programs and literature data. Several Tetrahedral phantoms were developed or adapted using computer-aided modeling techniques for these comparisons. Results: For human dose calculations, agreement of PARaDIM with OLINDA 2.0 was good-within 10%-20% for most organs-despite geometric differences among the phantoms tested. Agreement with MIRDcell for cell-level S value calculations was within 5% in most cases. Conclusion: PARaDIM extends the use of Monte Carlo dose calculations to the broader community in nuclear medicine by providing a user-friendly graphical user interface for calculation setup and execution. PARaDIM leverages the enhanced anatomic realism provided by advanced computational reference phantoms or bespoke image-derived phantoms to enable improved assessments of radiation doses in a variety of radiopharmaceutical use cases, research, and preclinical development. PARaDIM can be downloaded freely at www.paradim-dose.org.
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multi threading performance of geant4 mcnp6 and phits monte carlo codes for Tetrahedral Mesh geometry
Physics in Medicine and Biology, 2018Co-Authors: Min Cheol Han, Yeon Soo Yeom, Bangho Shin, Chan Hyeong Kim, Hyun Su Lee, Takuya FurutaAbstract:In this study, the multi-threading performance of the Geant4, MCNP6, and PHITS codes was evaluated as a function of the number of threads (N) and the complexity of the Tetrahedral-Mesh phantom. For this, three Tetrahedral-Mesh phantoms of varying complexity (simple, moderately complex, and highly complex) were prepared and implemented in the three different Monte Carlo codes, in photon and neutron transport simulations. Subsequently, for each case, the initialization time, calculation time, and memory usage were measured as a function of the number of threads used in the simulation. It was found that for all codes, the initialization time significantly increased with the complexity of the phantom, but not with the number of threads. Geant4 exhibited much longer initialization time than the other codes, especially for the complex phantom (MRCP). The improvement of computation speed due to the use of a multi-threaded code was calculated as the speed-up factor, the ratio of the computation speed on a multi-threaded code to the computation speed on a single-threaded code. Geant4 showed the best multi-threading performance among the codes considered in this study, with the speed-up factor almost linearly increasing with the number of threads, reaching ~30 when N = 40. PHITS and MCNP6 showed a much smaller increase of the speed-up factor with the number of threads. For PHITS, the speed-up factors were low when N = 40. For MCNP6, the increase of the speed-up factors was better, but they were still less than ~10 when N = 40. As for memory usage, Geant4 was found to use more memory than the other codes. In addition, compared to that of the other codes, the memory usage of Geant4 more rapidly increased with the number of threads, reaching as high as ~74 GB when N = 40 for the complex phantom (MRCP). It is notable that compared to that of the other codes, the memory usage of PHITS was much lower, regardless of both the complexity of the phantom and the number of threads, hardly increasing with the number of threads for the MRCP.
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Implementation of Tetrahedral-Mesh geometry in Monte Carlo radiation transport code PHITS.
Physics in medicine and biology, 2017Co-Authors: Takuya Furuta, Yeon Soo Yeom, Chan Hyeong Kim, Tatsuhiko Sato, Min Cheol Han, Justin L. Brown, Wesley E. BolchAbstract:A new function to treat Tetrahedral-Mesh geometry was implemented in the particle and heavy ion transport code systems. To accelerate the computational speed in the transport process, an original algorithm was introduced to initially prepare decomposition maps for the container box of the Tetrahedral-Mesh geometry. The computational performance was tested by conducting radiation transport simulations of 100 MeV protons and 1 MeV photons in a water phantom represented by Tetrahedral Mesh. The simulation was repeated with varying number of Meshes and the required computational times were then compared with those of the conventional voxel representation. Our results show that the computational costs for each boundary crossing of the region Mesh are essentially equivalent for both representations. This study suggests that the Tetrahedral-Mesh representation offers not only a flexible description of the transport geometry but also improvement of computational efficiency for the radiation transport. Due to the adaptability of tetrahedrons in both size and shape, dosimetrically equivalent objects can be represented by tetrahedrons with a much fewer number of Meshes as compared its voxelized representation. Our study additionally included dosimetric calculations using a computational human phantom. A significant acceleration of the computational speed, about 4 times, was confirmed by the adoption of a Tetrahedral Mesh over the traditional voxel Mesh geometry.
Chan Hyeong Kim - One of the best experts on this subject based on the ideXlab platform.
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poly2tet a computer program for conversion of computational human phantoms from polygonal Mesh to Tetrahedral Mesh
Journal of Radiological Protection, 2020Co-Authors: Haegin Han, Yeon Soo Yeom, Chansoo Choi, Sungho Moon, Bangho Shin, Chan Hyeong KimAbstract:As a geometrical format for computational human phantoms, Tetrahedral Mesh (TM) is known to have significant advantages over polygonal Mesh (PM), including higher compatibility with Monte Carlo radiation transport codes, higher computation speed, and the capability of modeling heterogeneous density variation in an organ of the phantom. In the present study, a computer program named POLY2TET was developed to convert the format of computational human phantoms from PM to TM and generate a sample source code or input file, as applicable, for the converted phantom to be used in some general-purpose Monte Carlo radiation transport codes (i.e. Geant4, PHITS, and MCNP6). The developed program was then tested using four existing high-fidelity PM phantoms. The computation speed, memory requirement, and initialisation time of the generated TM phantoms were also measured and compared with those of the original PM phantoms in Geant4. From the results of our test, it was concluded that the developed program successfully converts PM phantoms into the TM format. The organ doses calculated using the generated TM phantom for the three Monte Carlo codes all produced essentially identical dose values to those for the original PM phantoms in Geant4. The comparison of computation speed showed that compared to the original PM phantoms in Geant4, the TM phantoms in the three Monte Carlo codes were much faster in transporting the particles considered in the present study, i.e. by up to ∼2600 times for electron beams simulated in PHITS. The comparison of the memory requirement showed that the TM phantoms required more memory than the original PM phantoms, but, except for MCNP6, the memory required for the TM phantoms was still less than 12 GB, which typically is available in personal computers these days. For MCNP6, the required memory was much higher, i.e. 60-70 GB.
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paradim a phits based monte carlo tool for internal dosimetry with Tetrahedral Mesh computational phantoms
The Journal of Nuclear Medicine, 2019Co-Authors: Lukas M Carter, Chansoo Choi, Chan Hyeong Kim, Takuya Furuta, Tatsuhiko Sato, Justin L. Brown, Wesley E. Bolch, Troy Crawford, Pat ZanzonicoAbstract:Mesh-type and voxel-based computational phantoms comprise the current state of the art for internal dose assessment via Monte Carlo simulations but excel in different aspects, with Mesh-type phantoms offering advantages over their voxel counterparts in terms of their flexibility and realistic representation of detailed patient- or subject-specific anatomy. We have developed PARaDIM (pronounced "paradigm": Particle and Heavy Ion Transport Code System-Based Application for Radionuclide Dosimetry in Meshes), a freeware application for implementing Tetrahedral Mesh-type phantoms in absorbed dose calculations. It considers all medically relevant radionuclides, including α, β, γ, positron, and Auger/conversion electron emitters, and handles calculation of mean dose to individual regions, as well as 3-dimensional dose distributions for visualization and analysis in a variety of medical imaging software. This work describes the development of PARaDIM, documents the measures taken to test and validate its performance, and presents examples of its uses. Methods: Human, small-animal, and cell-level dose calculations were performed with PARaDIM and the results compared with those of widely accepted dosimetry programs and literature data. Several Tetrahedral phantoms were developed or adapted using computer-aided modeling techniques for these comparisons. Results: For human dose calculations, agreement of PARaDIM with OLINDA 2.0 was good-within 10%-20% for most organs-despite geometric differences among the phantoms tested. Agreement with MIRDcell for cell-level S value calculations was within 5% in most cases. Conclusion: PARaDIM extends the use of Monte Carlo dose calculations to the broader community in nuclear medicine by providing a user-friendly graphical user interface for calculation setup and execution. PARaDIM leverages the enhanced anatomic realism provided by advanced computational reference phantoms or bespoke image-derived phantoms to enable improved assessments of radiation doses in a variety of radiopharmaceutical use cases, research, and preclinical development. PARaDIM can be downloaded freely at www.paradim-dose.org.
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multi threading performance of geant4 mcnp6 and phits monte carlo codes for Tetrahedral Mesh geometry
Physics in Medicine and Biology, 2018Co-Authors: Min Cheol Han, Yeon Soo Yeom, Bangho Shin, Chan Hyeong Kim, Hyun Su Lee, Takuya FurutaAbstract:In this study, the multi-threading performance of the Geant4, MCNP6, and PHITS codes was evaluated as a function of the number of threads (N) and the complexity of the Tetrahedral-Mesh phantom. For this, three Tetrahedral-Mesh phantoms of varying complexity (simple, moderately complex, and highly complex) were prepared and implemented in the three different Monte Carlo codes, in photon and neutron transport simulations. Subsequently, for each case, the initialization time, calculation time, and memory usage were measured as a function of the number of threads used in the simulation. It was found that for all codes, the initialization time significantly increased with the complexity of the phantom, but not with the number of threads. Geant4 exhibited much longer initialization time than the other codes, especially for the complex phantom (MRCP). The improvement of computation speed due to the use of a multi-threaded code was calculated as the speed-up factor, the ratio of the computation speed on a multi-threaded code to the computation speed on a single-threaded code. Geant4 showed the best multi-threading performance among the codes considered in this study, with the speed-up factor almost linearly increasing with the number of threads, reaching ~30 when N = 40. PHITS and MCNP6 showed a much smaller increase of the speed-up factor with the number of threads. For PHITS, the speed-up factors were low when N = 40. For MCNP6, the increase of the speed-up factors was better, but they were still less than ~10 when N = 40. As for memory usage, Geant4 was found to use more memory than the other codes. In addition, compared to that of the other codes, the memory usage of Geant4 more rapidly increased with the number of threads, reaching as high as ~74 GB when N = 40 for the complex phantom (MRCP). It is notable that compared to that of the other codes, the memory usage of PHITS was much lower, regardless of both the complexity of the phantom and the number of threads, hardly increasing with the number of threads for the MRCP.
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Implementation of Tetrahedral-Mesh geometry in Monte Carlo radiation transport code PHITS.
Physics in medicine and biology, 2017Co-Authors: Takuya Furuta, Yeon Soo Yeom, Chan Hyeong Kim, Tatsuhiko Sato, Min Cheol Han, Justin L. Brown, Wesley E. BolchAbstract:A new function to treat Tetrahedral-Mesh geometry was implemented in the particle and heavy ion transport code systems. To accelerate the computational speed in the transport process, an original algorithm was introduced to initially prepare decomposition maps for the container box of the Tetrahedral-Mesh geometry. The computational performance was tested by conducting radiation transport simulations of 100 MeV protons and 1 MeV photons in a water phantom represented by Tetrahedral Mesh. The simulation was repeated with varying number of Meshes and the required computational times were then compared with those of the conventional voxel representation. Our results show that the computational costs for each boundary crossing of the region Mesh are essentially equivalent for both representations. This study suggests that the Tetrahedral-Mesh representation offers not only a flexible description of the transport geometry but also improvement of computational efficiency for the radiation transport. Due to the adaptability of tetrahedrons in both size and shape, dosimetrically equivalent objects can be represented by tetrahedrons with a much fewer number of Meshes as compared its voxelized representation. Our study additionally included dosimetric calculations using a computational human phantom. A significant acceleration of the computational speed, about 4 times, was confirmed by the adoption of a Tetrahedral Mesh over the traditional voxel Mesh geometry.
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new approach based on Tetrahedral Mesh geometry for accurate 4d monte carlo patient dose calculation
Physics in Medicine and Biology, 2015Co-Authors: Min Cheol Han, Yeon Soo Yeom, Chan Hyeong Kim, Seonghoon Kim, Jason W SohnAbstract:In the present study, to achieve accurate 4D Monte Carlo dose calculation in radiation therapy, we devised a new approach that combines (1) modeling of the patient body using Tetrahedral-Mesh geometry based on the patient's 4D CT data, (2) continuous movement/deformation of the Tetrahedral patient model by interpolation of deformation vector fields acquired through deformable image registration, and (3) direct transportation of radiation particles during the movement and deformation of the Tetrahedral patient model. The results of our feasibility study show that it is certainly possible to construct 4D patient models (= phantoms) with sufficient accuracy using the Tetrahedral-Mesh geometry and to directly transport radiation particles during continuous movement and deformation of the Tetrahedral patient model. This new approach not only produces more accurate dose distribution in the patient but also replaces the current practice of using multiple 3D voxel phantoms and combining multiple dose distributions after Monte Carlo simulations. For routine clinical application of our new approach, the use of fast automatic segmentation algorithms is a must. In order to achieve, simultaneously, both dose accuracy and computation speed, the number of tetrahedrons for the lungs should be optimized. Although the current computation speed of our new 4D Monte Carlo simulation approach is slow (i.e. ~40 times slower than that of the conventional dose accumulation approach), this problem is resolvable by developing, in Geant4, a dedicated navigation class optimized for particle transportation in Tetrahedral-Mesh geometry.
Kenji Shimada - One of the best experts on this subject based on the ideXlab platform.
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converting a Tetrahedral Mesh to a prism Tetrahedral hybrid Mesh for fem accuracy and efficiency
International Journal for Numerical Methods in Engineering, 2009Co-Authors: Soji Yamakawa, Kenji ShimadaAbstract:This paper presents a computational method for converting a Tetrahedral Mesh to a prism–Tetrahedral hybrid Mesh for improved solution accuracy and computational efficiency of finite element analysis. The proposed method performs this conversion by inserting layers of prism elements and deleting Tetrahedral elements in sweepable sub-domains, in which cross-sections remain topologically identical and geometrically similar along a certain sweeping path. The total number of finite elements is reduced because roughly three Tetrahedral elements are converted to one prism element. The solution accuracy of the finite element analysis improves since a prism element yields a more accurate solution than a Tetrahedral element due to the presence of higher-order terms in the shape function. Only previously known method for creating such a prism–Tetrahedral hybrid Mesh was to manually decompose a target volume into sweepable and non-sweepable sub-volumes and Mesh each of the sub-volumes separately. Unlike the previous method, the proposed method starts from a cross-section of a Tetrahedral Mesh and replaces the Tetrahedral elements with layers of prism elements until prescribed quality criteria can no longer be satisfied. A series of computational fluid dynamics simulations and structural analyses have been conducted, and the results verified a better performance of prism–Tetrahedral hybrid Mesh. Copyright © 2009 John Wiley & Sons, Ltd.
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converting a Tetrahedral Mesh to a prism Tetrahedral hybrid Mesh for fem accuracy and efficiency
Solid and Physical Modeling, 2008Co-Authors: Soji Yamakawa, Kenji ShimadaAbstract:This paper presents a computational method for converting a Tetrahedral Mesh to a prism-Tetrahedral hybrid Mesh for improved solution accuracy and computational efficiency of finite element analysis. The proposed method inserts layers of prism elements and deletes Tetrahedral elements in sweepable sub-domains, in which cross-sections remain topologically identical and geometrically similar along a certain sweeping path. The total number of finite elements is reduced because roughly three Tetrahedral elements are converted to one prism element. The solution accuracy of the finite element analysis improves since a prism element yields a more accurate solution than a Tetrahedral element. Only previously known method for creating such a prism-Tetrahedral Mesh was to manually decompose a target volume into sweepable and non-sweepable sub-volumes and Mesh each sub-volume separately. The proposed method starts from a cross-section of a Tetrahedral Mesh and replaces the Tetrahedral elements with layers of prism elements until prescribed quality criteria can no longer be satisfied. The method applies a sequence of edge-collapse, local-transformation, and smoothing operations to remove or displace nodes located within the volume to be replaced with a layer of prism elements. Series of computational fluid dynamics simulations and structural analyses have been conducted, and the results verified a better performance of prismTetrahedral hybrid Mesh in finite element simulations.
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hex dominant Mesh generation with directionality control via packing rectangular solid cells
Geometric Modeling and Processing, 2002Co-Authors: Soji Yamakawa, Kenji ShimadaAbstract:A new computational method that creates a hex-dominant Mesh of an arbitrary 3D geometric domain is presented. The proposed method generates a high-quality hex-dominant Mesh by: (1) controlling the directionality of the output hex-dominant Mesh; and (2) avoiding ill-shaped elements induced by nodes located too closely to each other. The proposed method takes a 3D geometric domain as input and creates a hex-dominant Mesh that consists of mostly hexahedral elements with additional prism elements and Tetrahedral elements. The proposed method packs rectangular solid cells on the boundary of and inside the input domain to obtain ideal node locations for a hex-dominant Mesh. Each cell has a potential energy field that mimics a body centered cubic (BCC) structure, and the cells are moved to stable positions by a physically-based simulation. The simulation mimics the formation of a crystal pattern so that the centers of the cells give ideal node locations for a hex-dominant Mesh. The domain is then Meshed into a Tetrahedral Mesh by the advancing front method, and finally the Tetrahedral Mesh is converted to a hex-dominant Mesh by merging some tetrahedrons.
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high quality anisotropic Tetrahedral Mesh generation via ellipsoidal bubble packing
IMR, 2000Co-Authors: Soji Yamakawa, Kenji ShimadaAbstract:This paper presents a new computational method for anisotropic Tetrahedral Meshing that (1) can control shapes of the elements by an arbitrary anisotropy function, and (2) can avoid ill-shaped elements induced from poorly distributed node locations. Our method creates a Tetrahedral Mesh in two steps. First our method obtains node locations through a physically based particle simulation, which we call 'bubble packing.' Ellipsoidal bubbles are closely packed on the boundary and inside a geometric domain, and nodes are placed at the centers of the bubbles. Our method then connects the nodes to create a tet Mesh by the advancing front method. Experimental results show that our method can create a high quality anisotropic Tetrahedral Mesh that conforms well to the input anisotropy.
