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Adaptive skin meshes coarsening for biomolecular simulation

Xinwei Shi, Patrice Koehl
2011 Computer Aided Geometric Design  
Each coarser surface mesh is adaptive to the surface curvature and maintains the topology of the skin surface with guaranteed mesh quality.  ...  In this paper, we present efficient algorithms for generating hierarchical molecular skin meshes with decreasing size and guaranteed quality.  ...  The coarse surface meshes are adaptive to the surface curvature and have guaranteed mesh quality and topology.  ... 
doi:10.1016/j.cagd.2011.04.001 pmid:21779137 pmcid:PMC3138625 fatcat:vnf4s6wgo5d57ilcnjcd6juy2i

Automatic All Quadrilateral Mesh Adaption through Refinement and Coarsening [chapter]

Bret D. Anderson, Steven E. Benzley, Steven J. Owen
2009 Proceedings of the 18th International Meshing Roundtable  
Given a sizing function, this method modifies the mesh by combining template-based quadrilateral refinement methods with recent developments in localized quadrilateral coarsening and quality improvement  ...  In contrast, we introduce a new method that incorporates both conformal refinement and coarsening strategies on an existing mesh of any density or configuration.  ...  This shaded region is coarsened and the resulting mesh topology can be seen in Figure 8 (b).  ... 
doi:10.1007/978-3-642-04319-2_32 dblp:conf/imr/AndersonBO09 fatcat:ehrkd4ytcbdepkz6ka5qtmz4oa

Adaptive mesh coarsening for quadrilateral and hexahedral meshes

Jason F. Shepherd, Mark W. Dewey, Adam C. Woodbury, Steven E. Benzley, Matthew L. Staten, Steven J. Owen
2010 Finite elements in analysis and design  
Mesh adaptation methods can improve the efficiency and accuracy of solutions to computational modeling problems.  ...  However, due to the added complexity of maintaining and satisfying constraints in quadrilateral and hexahedral mesh topology, little research has occurred in the area of coarsening or simplification.  ...  Element quality following coarsening remains high and is outlined in Table 3 . Figure 17 uses the same surface geometry, but with a much finer mesh.  ... 
doi:10.1016/j.finel.2009.06.024 fatcat:lal3ccsktrcurelvjyei2rjw3e

Approximated Centroidal Voronoi Diagrams for Uniform Polygonal Mesh Coarsening

Sebastien Valette, Jean-Marc Chassery
2004 Computer graphics forum (Print)  
The mesh topology is also simplified by the clustering algorithm. Based on a mathematical framework, our algorithm is easy to implement, and has low memory requirements.  ...  The clustering provides an efficient way to construct uniform tessellations, and therefore leads to uniform coarsening of polygonal meshes, when the output triangulation has many fewer elements than the  ...  The authors also thank Pierre Alliez and Cédric Gérot for their helpful comments on the paper.  ... 
doi:10.1111/j.1467-8659.2004.00769.x fatcat:gvczyo6hhnejrobfr3jnsjpx54

Unstructured Geometric Multigrid in Two and Three Dimensions on Complex and Graded Meshes [article]

Peter R. Brune and Matthew G. Knepley and L. Ridgway Scott
2011 arXiv   pre-print
We introduce a simplification of a general topologically-motivated mesh coarsening algorithm for use in creating hierarchies of meshes for geometric unstructured multigrid methods.  ...  The connections between the guarantees of this technique and the quality criteria necessary for multigrid methods for non-quasi-uniform problems are noted.  ...  Meshing issues still exist, as the local remeshing can be quite costly in 3D. There are several ways the remeshing could be improved, both in terms of efficiency and mesh quality guarantees.  ... 
arXiv:1104.0261v2 fatcat:2aktv67x2jda5pur7s3uc6drb4

3D anisotropic mesh adaptation by mesh modification

Xiangrong Li, Mark S. Shephard, Mark W. Beall
2005 Computer Methods in Applied Mechanics and Engineering  
This paper describes an effective anisotropic mesh adaptation procedure for general 3D geometries using mesh modification operations.  ...  The procedure consists of four interacted high level components: refinement, coarsening, projecting boundary vertices and shape correction.  ...  Tezduyar for providing the surface mesh of the parachute problem and Nicolas Chevaugeon for providing the pictures of the cannon blast problem.  ... 
doi:10.1016/j.cma.2004.11.019 fatcat:4dcamgx3o5bhpbrmxpcje5y6oe

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation

Zeyun Yu, Michael J. Holst, Yuhui Cheng, J.Andrew McCammon
2008 Journal of Molecular Graphics and Modelling  
The approaches presented and their implementations are also applicable to other types of inputs such as 3D scalar volumes and triangular surface meshes with low quality, and hence can be used for generation  ...  Experiments on a number of molecules are demonstrated, showing that our methods possess several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface meshes  ...  Along with the mesh coarsening, a normalbased surface mesh smoothing technique is employed to guarantee the smoothness of the meshes while they are being coarsened.  ... 
doi:10.1016/j.jmgm.2008.01.007 pmid:18337134 fatcat:w63cd6wh2vhnvejm2dhe2qadq4

A simple and flexible framework to adapt dynamic meshes

Fernando de Goes, Siome Goldenstein, Luiz Velho
2008 Computers & graphics  
In this paper we present a simple and flexible framework to adapt dynamic meshes following deformable surfaces.  ...  Many graphics applications represent deformable surfaces through dynamic meshes. To be consistent during deformations, the dynamic meshes require an adaptation process.  ...  Supplementary data Supplementary data associated with this article can be found in the online version of doi:10.1016/j.cag.2008. 01.009.  ... 
doi:10.1016/j.cag.2008.01.009 fatcat:3wdbup66bvawbctt5x3uyhvryi

Adaptive SQP Method for Shape Optimization [chapter]

P. Morin, R. H. Nochetto, M. S. Pauletti, M. Verani
2010 Numerical Mathematics and Advanced Applications 2009  
Inexactness is a consequence of using adaptive finite element methods (AFEM) to approximate the state equation, update the boundary, and compute the geometric functional.  ...  We present a novel algorithm that uses a dynamic tolerance and equidistributes the errors due to shape optimization and discretization, thereby leading to coarse resolution in the early stages and fine  ...  The algorithm, described in [5] , guarantees volume conservation to machine precision in each time iteration and is well suited to be utilized inside the Armijo condition loop.  ... 
doi:10.1007/978-3-642-11795-4_71 fatcat:xjvv6b2fnbbmrp6i5fh2vtcate

Localized Quadrilateral Coarsening

Joel Daniels, Claudio T. Silva, Elaine Cohen
2009 Computer graphics forum (Print)  
In this paper we introduce a coarsening algorithm for quadrilateral meshes that generates quality, quad-only connectivity during level-of-coarsening creation.  ...  A novel aspect of this work is development and implementation of a localized adaptation of the polychord collapse operator to better control and preserve important surface components.  ...  We thank Jason Shepherd and the AIM@SHAPE project for access to 3D models used in our research.  ... 
doi:10.1111/j.1467-8659.2009.01520.x fatcat:vgjzp37ofzg4feyntykwivndqe

High-fidelity geometric modeling for biomedical applications

Zeyun Yu, Michael J. Holst, J. Andrew McCammon
2008 Finite elements in analysis and design  
The main goal of our work presented is to generate high quality and smooth surface triangulations from the aforementioned inputs, and to reduce the mesh sizes by mesh coarsening.  ...  Experiments on a number of bio-structures are demonstrated, showing that our approach possesses several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface  ...  Along with the mesh coarsening, a normalbased surface mesh smoothing technique is employed to guarantee the smoothness of the meshes while they are being coarsened.  ... 
doi:10.1016/j.finel.2008.03.004 fatcat:wmscxdca55balhoghcwty4ivee

Efficient adaptive meshing of parametric models

Alla Sheffer, Alper Üngör
2001 Proceedings of the sixth ACM symposium on Solid modeling and applications - SMA '01  
However, when generating the finite-element mesh of the model for simulation and analysis, most meshing tools ignore the parametric information and use only the boundary representation of the model for  ...  meshing.  ...  Acknowledgments The work reported here was supported, in part, by the Center for Process Simulation and Design (NSF DMS 98-73945) and the Center for Simulation of Advanced Rockets (DOE LLNL B341494).  ... 
doi:10.1145/376957.376964 dblp:conf/sma/ShefferU01 fatcat:vs3yryrhuvegdikgxm3ko56iey

A new hybrid adaptive mesh algorithm based on Voronoi tessellations and equi-distribution principle: Algorithms and numerical experiments

Shaolin Mao
2015 Computers & Fluids  
The algorithm consists of several unique features: first, dynamic change of mesh topology (reconnection of nodes) is realized through refinement and coarsening iterations with specific feature (i.e.  ...  smoothing for the purpose of speed-up of the adaptive iterations; third, a new marking strategy with double threshold values guarantee the convergence of adaptive iterations.  ...  The author would like to thank anonymous reviewers for their time and valuable comments which help us to clarify the confusion and correct errors during the preparation. References  ... 
doi:10.1016/j.compfluid.2014.12.021 fatcat:iuvospvurrdhbnf6es2dawt3nq

Parallel Adaptive Boundary Layer Meshing for CFD Analysis [chapter]

Aleksandr Ovcharenko, Kedar Chitale, Onkar Sahni, Kenneth E. Jansen, Mark S. Shephard
2013 Proceedings of the 21st International Meshing Roundtable  
The parallel mesh adaptation algorithm operates with local mesh modification operations developed for both unstructured and boundary layer parts of the mesh.  ...  This paper describes a parallel procedure for anisotropic mesh adaptation with boundary layers for use in scalable CFD simulations.  ...  and increasing the mesh quality.  ... 
doi:10.1007/978-3-642-33573-0_26 dblp:conf/imr/OvcharenkoCSJS12 fatcat:hpx2cweva5ghbmq2uetelp3isu

Adaptive Treelet Meshes for Efficient Streak-Surface Visualization on the GPU [article]

Raphael Fuchs, Benjamin Schindler, Robert Carnecky, Jürgen Waser, Yun Jang, Ronny Peikert
2012 International Symposium on Vision, Modeling, and Visualization  
We describe a novel adaptive mesh representation for streak-surfaces. The surface is represented as a mesh of small trees of initial depth zero (treelets).  ...  This mesh representation allows for efficient integration, refinement, coarsening and appending of surface patches utilizing the computational capacities of modern GPUs.  ...  Streak-surfaces are a class of especially relevant material surfaces since they are related to time-dependent topological structures and can convey important topological information about the flow [SW10  ... 
doi:10.2312/pe/vmv/vmv12/119-126 dblp:conf/vmv/FuchsSCWYP12 fatcat:l6umcrrdgve2riwsqsw7kuxfwy
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